############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Aug 25 15:13:12 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Aug 25 15:13:23 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/gulrotkake/groel_md/1XCK/electrostatics/E434K_apo_heptamer_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54894 atoms Valist_getStatistics: Max atom coordinate: (108.044, 134.353, 297.511) Valist_getStatistics: Min atom coordinate: (-21.715, -9.874, 152.985) Valist_getStatistics: Molecule center: (43.1645, 62.2395, 225.248) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1645 62.1395 225.19 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1645 62.1395 225.19 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.17193, 1.3018, 1.30371 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.793536, 0.869932, 0.871057 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.67712, 0.668253, 0.668135 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1645 62.1395 225.19 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 155.67 187.112 350.346 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -69.3407 -62.8334 100.033 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 119.344 145.653 308.811 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -33.015 -21.374 141.568 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 119.344 145.653 308.811 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -33.015 -21.374 141.568 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 78.8976 Vpbe_ctor2: solute dimensions = 132.359 x 147.027 x 147.243 Vpbe_ctor2: solute charge = -111.966 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (141.971, 156.439, 156.738) Vclist_setupGrid: Grid lower corner = (-27.821, -15.98, 146.879) Vclist_assignAtoms: Have 11141890 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.721000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.500000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.370000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.139000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.217559e-02 PMG: contraction number = 4.217559e-02 PMG: iteration = 2 PMG: relative residual = 5.501602e-03 PMG: contraction number = 1.304452e-01 PMG: iteration = 3 PMG: relative residual = 9.233619e-04 PMG: contraction number = 1.678351e-01 PMG: iteration = 4 PMG: relative residual = 1.856252e-04 PMG: contraction number = 2.010319e-01 PMG: iteration = 5 PMG: relative residual = 4.399229e-05 PMG: contraction number = 2.369953e-01 PMG: iteration = 6 PMG: relative residual = 1.202384e-05 PMG: contraction number = 2.733170e-01 PMG: iteration = 7 PMG: relative residual = 3.668395e-06 PMG: contraction number = 3.050934e-01 PMG: iteration = 8 PMG: relative residual = 1.212239e-06 PMG: contraction number = 3.304550e-01 PMG: iteration = 9 PMG: relative residual = 4.231602e-07 PMG: contraction number = 3.490731e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.696000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.062000e+01 Vpmg_setPart: lower corner = (-69.3407, -62.8334, 100.033) Vpmg_setPart: upper corner = (155.67, 187.112, 350.346) Vpmg_setPart: actual minima = (-69.3407, -62.8334, 100.033) Vpmg_setPart: actual maxima = (155.67, 187.112, 350.346) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 78.8976 Vpbe_ctor2: solute dimensions = 132.359 x 147.027 x 147.243 Vpbe_ctor2: solute charge = -111.966 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (141.971, 156.439, 156.738) Vclist_setupGrid: Grid lower corner = (-27.821, -15.98, 146.879) Vclist_assignAtoms: Have 11141890 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -33.015, -21.374, 141.568 VPMG::focusFillBound -- New mesh maxs = 119.344, 145.653, 308.811 VPMG::focusFillBound -- Old mesh mins = -69.3407, -62.8334, 100.033 VPMG::focusFillBound -- Old mesh maxs = 155.67, 187.112, 350.346 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.021000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.500000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.180000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.421700e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 5.697237e-02 PMG: contraction number = 5.697237e-02 PMG: iteration = 2 PMG: relative residual = 7.271329e-03 PMG: contraction number = 1.276290e-01 PMG: iteration = 3 PMG: relative residual = 1.121451e-03 PMG: contraction number = 1.542292e-01 PMG: iteration = 4 PMG: relative residual = 1.963027e-04 PMG: contraction number = 1.750435e-01 PMG: iteration = 5 PMG: relative residual = 3.926831e-05 PMG: contraction number = 2.000396e-01 PMG: iteration = 6 PMG: relative residual = 9.856540e-06 PMG: contraction number = 2.510050e-01 PMG: iteration = 7 PMG: relative residual = 2.914100e-06 PMG: contraction number = 2.956514e-01 PMG: iteration = 8 PMG: relative residual = 9.708809e-07 PMG: contraction number = 3.331666e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.045000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.407000e+01 Vpmg_setPart: lower corner = (-33.015, -21.374, 141.568) Vpmg_setPart: upper corner = (119.344, 145.653, 308.811) Vpmg_setPart: actual minima = (-33.015, -21.374, 141.568) Vpmg_setPart: actual maxima = (119.344, 145.653, 308.811) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.992000e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Aug 25 15:27:05 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Aug 25 15:27:14 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/gulrotkake/groel_md/1XCK/electrostatics/E461K_apo_heptamer_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (225, 129, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54894 atoms Valist_getStatistics: Max atom coordinate: (172.145, 148.539, 198.722) Valist_getStatistics: Min atom coordinate: (23.617, 71.019, 51.424) Valist_getStatistics: Molecule center: (97.881, 109.779, 125.073) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 97.881 109.779 125.073 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 97.881 109.779 125.073 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.14695, 1.06409, 1.13762 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.763964, 0.782188, 0.758473 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666081, 0.735074, 0.66672 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 97.881 109.779 125.073 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 226.34 177.881 252.486 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -30.5778 41.677 -2.3403 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 183.445 159.839 210.022 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 12.317 59.719 40.124 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 183.445 159.839 210.022 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 12.317 59.719 40.124 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.0719 Vpbe_ctor2: solute dimensions = 151.128 x 80.12 x 149.898 Vpbe_ctor2: solute charge = -111.966 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (160.74, 89.732, 159.51) Vclist_setupGrid: Grid lower corner = (17.511, 64.913, 45.318) Vclist_assignAtoms: Have 15064540 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 225, ny = 129, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 29, nyc = 17, nzc = 29 Vpmg_ctor2: PMG chose nf = 6530625, nc = 14297 Vpmg_ctor2: PMG chose narr = 7482124, narrc = 951499 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 84844497, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.598000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 6.900000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.460000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.115000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 5.271760e-02 PMG: contraction number = 5.271760e-02 PMG: iteration = 2 PMG: relative residual = 7.522135e-03 PMG: contraction number = 1.426874e-01 PMG: iteration = 3 PMG: relative residual = 1.812626e-03 PMG: contraction number = 2.409722e-01 PMG: iteration = 4 PMG: relative residual = 3.976584e-04 PMG: contraction number = 2.193825e-01 PMG: iteration = 5 PMG: relative residual = 1.273022e-04 PMG: contraction number = 3.201295e-01 PMG: iteration = 6 PMG: relative residual = 3.025463e-05 PMG: contraction number = 2.376599e-01 PMG: iteration = 7 PMG: relative residual = 1.056870e-05 PMG: contraction number = 3.493249e-01 PMG: iteration = 8 PMG: relative residual = 2.567541e-06 PMG: contraction number = 2.429383e-01 PMG: iteration = 9 PMG: relative residual = 9.160737e-07 PMG: contraction number = 3.567903e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 4.948000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.409000e+01 Vpmg_setPart: lower corner = (-30.5778, 41.677, -2.3403) Vpmg_setPart: upper corner = (226.34, 177.881, 252.486) Vpmg_setPart: actual minima = (-30.5778, 41.677, -2.3403) Vpmg_setPart: actual maxima = (226.34, 177.881, 252.486) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.0719 Vpbe_ctor2: solute dimensions = 151.128 x 80.12 x 149.898 Vpbe_ctor2: solute charge = -111.966 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (160.74, 89.732, 159.51) Vclist_setupGrid: Grid lower corner = (17.511, 64.913, 45.318) Vclist_assignAtoms: Have 15064540 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 225, ny = 129, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 29, nyc = 17, nzc = 29 Vpmg_ctor2: PMG chose nf = 6530625, nc = 14297 Vpmg_ctor2: PMG chose narr = 7482124, narrc = 951499 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 84844497, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 12.317, 59.719, 40.124 VPMG::focusFillBound -- New mesh maxs = 183.445, 159.839, 210.022 VPMG::focusFillBound -- Old mesh mins = -30.5778, 41.677, -2.3403 VPMG::focusFillBound -- Old mesh maxs = 226.34, 177.881, 252.486 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.933000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 6.800000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.210000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.344100e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 6.909245e-02 PMG: contraction number = 6.909245e-02 PMG: iteration = 2 PMG: relative residual = 9.280328e-03 PMG: contraction number = 1.343175e-01 PMG: iteration = 3 PMG: relative residual = 2.069160e-03 PMG: contraction number = 2.229620e-01 PMG: iteration = 4 PMG: relative residual = 4.758601e-04 PMG: contraction number = 2.299774e-01 PMG: iteration = 5 PMG: relative residual = 2.211637e-04 PMG: contraction number = 4.647662e-01 PMG: iteration = 6 PMG: relative residual = 6.262849e-05 PMG: contraction number = 2.831771e-01 PMG: iteration = 7 PMG: relative residual = 3.568835e-05 PMG: contraction number = 5.698421e-01 PMG: iteration = 8 PMG: relative residual = 1.047322e-05 PMG: contraction number = 2.934633e-01 PMG: iteration = 9 PMG: relative residual = 6.140396e-06 PMG: contraction number = 5.862950e-01 PMG: iteration = 10 PMG: relative residual = 1.828255e-06 PMG: contraction number = 2.977422e-01 PMG: iteration = 11 PMG: relative residual = 1.074652e-06 PMG: contraction number = 5.878022e-01 PMG: iteration = 12 PMG: relative residual = 3.239129e-07 PMG: contraction number = 3.014118e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.839000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.279000e+01 Vpmg_setPart: lower corner = (12.317, 59.719, 40.124) Vpmg_setPart: upper corner = (183.445, 159.839, 210.022) Vpmg_setPart: actual minima = (12.317, 59.719, 40.124) Vpmg_setPart: actual maxima = (183.445, 159.839, 210.022) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.085500e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Sat Sep 25 13:36:40 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_apo_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (97, 97, 97) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Sat Sep 25 13:48:15 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (97, 97, 97) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 109998 atoms Valist_getStatistics: Max atom coordinate: (77.814, 120.756, 86.513) Valist_getStatistics: Min atom coordinate: (-70.371, -30.892, -60.367) Valist_getStatistics: Molecule center: (3.7215, 44.932, 13.073) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 52.047 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 52.047 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.07431, 1.35327, 1.08945 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.840281, 1.00438, 0.849187 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.782158, 0.742183, 0.779463 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 52.047 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 94.7614 117.004 96.0527 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -8.37245 -12.91 -8.5347 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 83.528 100.257 84.52 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 2.861 3.837 2.998 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 83.528 100.257 84.52 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 2.861 3.837 2.998 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 94.9153 Vpbe_ctor2: solute dimensions = 148.185 x 151.648 x 146.88 Vpbe_ctor2: solute charge = 109998 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (155.285, 158.748, 153.98) Vclist_setupGrid: Grid lower corner = (-73.921, -34.442, -63.917) Vclist_assignAtoms: Have 9190217 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 78.5398 Vacc_storeParms: Using 792-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 97, ny = 97, nz = 97 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 912673, nc = 2197 Vpmg_ctor2: PMG chose narr = 1048144, narrc = 135471 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 13127137, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.510000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 9.000000e-02 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.000000e-01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.100000e+00 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.978065e+10 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.750000e+00 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.891210e+09 PMG: contraction number = , 5.891210e+09 NEWTON: attempting damping, relres = 1.065090e-01 NEWTON: attempting damping, relres = 5.524018e-01 NEWTON: damping accepted, relres = 1.065090e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.065090e-01 PMG: contraction number = 1.065090e-01 NEWTON: using errtol_s: 5.302089e+09 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.470000e+00 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.960620e+08 PMG: contraction number = , 6.960620e+08 PMG: iteration = 2 PMG: relative residual = 1.258432e-02 PMG: contraction number = 1.181526e-01 NEWTON: using errtol_s: 6.264558e+08 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.720000e+00 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.723018e+07 PMG: contraction number = , 9.723018e+07 PMG: iteration = 3 PMG: relative residual = 1.757855e-03 PMG: contraction number = 1.396861e-01 NEWTON: using errtol_s: 8.750716e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.880000e+00 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.550131e+07 PMG: contraction number = , 1.550131e+07 PMG: iteration = 4 PMG: relative residual = 2.802531e-04 PMG: contraction number = 1.594290e-01 NEWTON: using errtol_s: 1.395118e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.662684e+06 PMG: contraction number = , 2.662684e+06 PMG: iteration = 5 PMG: relative residual = 4.813950e-05 PMG: contraction number = 1.717715e-01 NEWTON: using errtol_s: 2.396416e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.270000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.759820e+05 PMG: contraction number = , 4.759820e+05 PMG: iteration = 6 PMG: relative residual = 8.605427e-06 PMG: contraction number = 1.787602e-01 NEWTON: using errtol_s: 4.283838e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.393000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.682287e+04 PMG: contraction number = , 8.682287e+04 PMG: iteration = 7 PMG: relative residual = 1.569698e-06 PMG: contraction number = 1.824079e-01 NEWTON: using errtol_s: 7.814058e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.599614e+04 PMG: contraction number = , 1.599614e+04 PMG: iteration = 8 PMG: relative residual = 2.891993e-07 PMG: contraction number = 1.842388e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.083000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.131000e+01 Vpmg_setPart: lower corner = (-8.37245, -12.91, -8.5347) Vpmg_setPart: upper corner = (94.7614, 117.004, 96.0527) Vpmg_setPart: actual minima = (-8.37245, -12.91, -8.5347) Vpmg_setPart: actual maxima = (94.7614, 117.004, 96.0527) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 94.9153 Vpbe_ctor2: solute dimensions = 148.185 x 151.648 x 146.88 Vpbe_ctor2: solute charge = 109998 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (155.285, 158.748, 153.98) Vclist_setupGrid: Grid lower corner = (-73.921, -34.442, -63.917) Vclist_assignAtoms: Have 9190217 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 78.5398 Vacc_storeParms: Using 792-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 97, ny = 97, nz = 97 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 912673, nc = 2197 Vpmg_ctor2: PMG chose narr = 1048144, narrc = 135471 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 13127137, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 2.861, 3.837, 2.998 VPMG::focusFillBound -- New mesh maxs = 83.528, 100.257, 84.52 VPMG::focusFillBound -- Old mesh mins = -8.37245, -12.91, -8.5347 VPMG::focusFillBound -- Old mesh maxs = 94.7614, 117.004, 96.0527 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.080000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 9.000000e-02 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.300000e-01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.199796e+10 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.052250e+09 PMG: contraction number = , 5.052250e+09 NEWTON: attempting damping, relres = 1.082678e-01 NEWTON: attempting damping, relres = 5.534844e-01 NEWTON: damping accepted, relres = 1.082678e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.082678e-01 PMG: contraction number = 1.082678e-01 NEWTON: using errtol_s: 4.547025e+09 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.962000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.735223e+08 PMG: contraction number = , 5.735223e+08 PMG: iteration = 2 PMG: relative residual = 1.229036e-02 PMG: contraction number = 1.135182e-01 NEWTON: using errtol_s: 5.161701e+08 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.328473e+07 PMG: contraction number = , 7.328473e+07 PMG: iteration = 3 PMG: relative residual = 1.570463e-03 PMG: contraction number = 1.277801e-01 NEWTON: using errtol_s: 6.595626e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.191000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.003390e+07 PMG: contraction number = , 1.003390e+07 PMG: iteration = 4 PMG: relative residual = 2.150225e-04 PMG: contraction number = 1.369166e-01 NEWTON: using errtol_s: 9.030508e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.318000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.469484e+06 PMG: contraction number = , 1.469484e+06 PMG: iteration = 5 PMG: relative residual = 3.149046e-05 PMG: contraction number = 1.464519e-01 NEWTON: using errtol_s: 1.322535e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.433000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.244401e+05 PMG: contraction number = , 2.244401e+05 PMG: iteration = 6 PMG: relative residual = 4.809663e-06 PMG: contraction number = 1.527340e-01 NEWTON: using errtol_s: 2.019960e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.547000e+01 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.511197e+04 PMG: contraction number = , 3.511197e+04 PMG: iteration = 7 PMG: relative residual = 7.524359e-07 PMG: contraction number = 1.564425e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.020000e+00 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.400000e+00 Vpmg_setPart: lower corner = (2.861, 3.837, 2.998) Vpmg_setPart: upper corner = (83.528, 100.257, 84.52) Vpmg_setPart: actual minima = (2.861, 3.837, 2.998) Vpmg_setPart: actual maxima = (83.528, 100.257, 84.52) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.774000e+01 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:24:26 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:24:57 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:25:19 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.970000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.400000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.350000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.146000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.203867e-02 PMG: contraction number = 9.203867e-02 PMG: iteration = 2 PMG: relative residual = 1.235397e-02 PMG: contraction number = 1.342258e-01 PMG: iteration = 3 PMG: relative residual = 3.251515e-03 PMG: contraction number = 2.631961e-01 PMG: iteration = 4 PMG: relative residual = 7.779779e-04 PMG: contraction number = 2.392663e-01 PMG: iteration = 5 PMG: relative residual = 3.709536e-04 PMG: contraction number = 4.768176e-01 PMG: iteration = 6 PMG: relative residual = 1.138415e-04 PMG: contraction number = 3.068888e-01 PMG: iteration = 7 PMG: relative residual = 6.299381e-05 PMG: contraction number = 5.533465e-01 PMG: iteration = 8 PMG: relative residual = 2.054304e-05 PMG: contraction number = 3.261120e-01 PMG: iteration = 9 PMG: relative residual = 1.143048e-05 PMG: contraction number = 5.564160e-01 PMG: iteration = 10 PMG: relative residual = 3.821412e-06 PMG: contraction number = 3.343179e-01 PMG: iteration = 11 PMG: relative residual = 2.099596e-06 PMG: contraction number = 5.494294e-01 PMG: iteration = 12 PMG: relative residual = 7.132159e-07 PMG: contraction number = 3.396919e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.573000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.908000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:25:54 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.210000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.290000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.964000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.296044e-01 PMG: contraction number = 1.296044e-01 PMG: iteration = 2 PMG: relative residual = 1.752819e-02 PMG: contraction number = 1.352438e-01 PMG: iteration = 3 PMG: relative residual = 3.141082e-03 PMG: contraction number = 1.792017e-01 PMG: iteration = 4 PMG: relative residual = 6.355540e-04 PMG: contraction number = 2.023360e-01 PMG: iteration = 5 PMG: relative residual = 1.921930e-04 PMG: contraction number = 3.024023e-01 PMG: iteration = 6 PMG: relative residual = 5.883113e-05 PMG: contraction number = 3.061045e-01 PMG: iteration = 7 PMG: relative residual = 2.591838e-05 PMG: contraction number = 4.405555e-01 PMG: iteration = 8 PMG: relative residual = 1.037723e-05 PMG: contraction number = 4.003812e-01 PMG: iteration = 9 PMG: relative residual = 5.068662e-06 PMG: contraction number = 4.884407e-01 PMG: iteration = 10 PMG: relative residual = 2.337104e-06 PMG: contraction number = 4.610890e-01 PMG: iteration = 11 PMG: relative residual = 1.140685e-06 PMG: contraction number = 4.880764e-01 PMG: iteration = 12 PMG: relative residual = 5.642622e-07 PMG: contraction number = 4.946694e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.446000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.781000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.386600e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:26:50 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.030000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.720000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.484859e-02 PMG: contraction number = 9.484859e-02 PMG: iteration = 2 PMG: relative residual = 1.387728e-02 PMG: contraction number = 1.463099e-01 PMG: iteration = 3 PMG: relative residual = 5.025394e-03 PMG: contraction number = 3.621310e-01 PMG: iteration = 4 PMG: relative residual = 1.701954e-03 PMG: contraction number = 3.386707e-01 PMG: iteration = 5 PMG: relative residual = 1.086154e-03 PMG: contraction number = 6.381808e-01 PMG: iteration = 6 PMG: relative residual = 4.919519e-04 PMG: contraction number = 4.529301e-01 PMG: iteration = 7 PMG: relative residual = 3.165704e-04 PMG: contraction number = 6.434987e-01 PMG: iteration = 8 PMG: relative residual = 1.551670e-04 PMG: contraction number = 4.901500e-01 PMG: iteration = 9 PMG: relative residual = 9.641661e-05 PMG: contraction number = 6.213732e-01 PMG: iteration = 10 PMG: relative residual = 4.890153e-05 PMG: contraction number = 5.071899e-01 PMG: iteration = 11 PMG: relative residual = 2.974743e-05 PMG: contraction number = 6.083128e-01 PMG: iteration = 12 PMG: relative residual = 1.534917e-05 PMG: contraction number = 5.159832e-01 PMG: iteration = 13 PMG: relative residual = 9.227034e-06 PMG: contraction number = 6.011421e-01 PMG: iteration = 14 PMG: relative residual = 4.804737e-06 PMG: contraction number = 5.207238e-01 PMG: iteration = 15 PMG: relative residual = 2.869176e-06 PMG: contraction number = 5.971557e-01 PMG: iteration = 16 PMG: relative residual = 1.501602e-06 PMG: contraction number = 5.233567e-01 PMG: iteration = 17 PMG: relative residual = 8.933127e-07 PMG: contraction number = 5.949064e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 7.601000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.981000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.040000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.100000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.600000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.308403e-01 PMG: contraction number = 1.308403e-01 PMG: iteration = 2 PMG: relative residual = 1.798493e-02 PMG: contraction number = 1.374571e-01 PMG: iteration = 3 PMG: relative residual = 3.998841e-03 PMG: contraction number = 2.223440e-01 PMG: iteration = 4 PMG: relative residual = 1.208122e-03 PMG: contraction number = 3.021181e-01 PMG: iteration = 5 PMG: relative residual = 6.757788e-04 PMG: contraction number = 5.593629e-01 PMG: iteration = 6 PMG: relative residual = 3.359785e-04 PMG: contraction number = 4.971723e-01 PMG: iteration = 7 PMG: relative residual = 2.245786e-04 PMG: contraction number = 6.684315e-01 PMG: iteration = 8 PMG: relative residual = 1.218076e-04 PMG: contraction number = 5.423831e-01 PMG: iteration = 9 PMG: relative residual = 8.054516e-05 PMG: contraction number = 6.612490e-01 PMG: iteration = 10 PMG: relative residual = 4.482449e-05 PMG: contraction number = 5.565138e-01 PMG: iteration = 11 PMG: relative residual = 2.923878e-05 PMG: contraction number = 6.522948e-01 PMG: iteration = 12 PMG: relative residual = 1.647713e-05 PMG: contraction number = 5.635367e-01 PMG: iteration = 13 PMG: relative residual = 1.065689e-05 PMG: contraction number = 6.467688e-01 PMG: iteration = 14 PMG: relative residual = 6.049021e-06 PMG: contraction number = 5.676159e-01 PMG: iteration = 15 PMG: relative residual = 3.891927e-06 PMG: contraction number = 6.433979e-01 PMG: iteration = 16 PMG: relative residual = 2.218809e-06 PMG: contraction number = 5.701055e-01 PMG: iteration = 17 PMG: relative residual = 1.422917e-06 PMG: contraction number = 6.412978e-01 PMG: iteration = 18 PMG: relative residual = 8.134154e-07 PMG: contraction number = 5.716533e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 8.221000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.566000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.870900e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:28:24 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (321, 385, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.336106, 0.350714, 0.340648 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.260209, 0.258385, 0.262881 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 321, ny = 385, nz = 321 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 41, nyc = 49, nzc = 41 Vpmg_ctor2: PMG chose nf = 39670785, nc = 82369 Vpmg_ctor2: PMG chose narr = 45392324, narrc = 5721539 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 618018025, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.264000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:33:25 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:33:58 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_apo_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (225, 225, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 109690 atoms Valist_getStatistics: Max atom coordinate: (77.814, 120.756, 86.513) Valist_getStatistics: Min atom coordinate: (-70.371, -30.892, -60.367) Valist_getStatistics: Molecule center: (3.7215, 44.932, 13.073) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 3.7215 44.932 13.073 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 3.7215 44.932 13.073 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.14435, 1.17063, 1.13445 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.762433, 0.777893, 0.756607 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666258, 0.664507, 0.66694 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 3.7215 44.932 13.073 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 131.889 176.043 140.131 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -124.446 -86.1788 -113.985 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 89.114 132.056 97.813 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -81.671 -42.192 -71.667 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 89.114 132.056 97.813 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -81.671 -42.192 -71.667 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 96.4153 Vpbe_ctor2: solute dimensions = 150.785 x 154.248 x 149.48 Vpbe_ctor2: solute charge = -251.926 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (160.397, 163.86, 159.092) Vclist_setupGrid: Grid lower corner = (-76.477, -36.998, -66.473) Vclist_assignAtoms: Have 19725309 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 225, ny = 225, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 29, nyc = 29, nzc = 29 Vpmg_ctor2: PMG chose nf = 11390625, nc = 24389 Vpmg_ctor2: PMG chose narr = 13043104, narrc = 1652479 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 154320561, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.719000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.200000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.480000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.873000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.849217e-02 PMG: contraction number = 4.849217e-02 PMG: iteration = 2 PMG: relative residual = 7.018459e-03 PMG: contraction number = 1.447339e-01 PMG: iteration = 3 PMG: relative residual = 1.679679e-03 PMG: contraction number = 2.393231e-01 PMG: iteration = 4 PMG: relative residual = 3.583651e-04 PMG: contraction number = 2.133533e-01 PMG: iteration = 5 PMG: relative residual = 1.204307e-04 PMG: contraction number = 3.360558e-01 PMG: iteration = 6 PMG: relative residual = 2.795360e-05 PMG: contraction number = 2.321137e-01 PMG: iteration = 7 PMG: relative residual = 1.058462e-05 PMG: contraction number = 3.786497e-01 PMG: iteration = 8 PMG: relative residual = 2.501851e-06 PMG: contraction number = 2.363666e-01 PMG: iteration = 9 PMG: relative residual = 9.881436e-07 PMG: contraction number = 3.949650e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 8.981000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.002900e+02 Vpmg_setPart: lower corner = (-124.446, -86.1788, -113.985) Vpmg_setPart: upper corner = (131.889, 176.043, 140.131) Vpmg_setPart: actual minima = (-124.446, -86.1788, -113.985) Vpmg_setPart: actual maxima = (131.889, 176.043, 140.131) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 96.4153 Vpbe_ctor2: solute dimensions = 150.785 x 154.248 x 149.48 Vpbe_ctor2: solute charge = -251.926 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (160.397, 163.86, 159.092) Vclist_setupGrid: Grid lower corner = (-76.477, -36.998, -66.473) Vclist_assignAtoms: Have 19725309 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 225, ny = 225, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 29, nyc = 29, nzc = 29 Vpmg_ctor2: PMG chose nf = 11390625, nc = 24389 Vpmg_ctor2: PMG chose narr = 13043104, narrc = 1652479 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 154320561, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -81.671, -42.192, -71.667 VPMG::focusFillBound -- New mesh maxs = 89.114, 132.056, 97.813 VPMG::focusFillBound -- Old mesh mins = -124.446, -86.1788, -113.985 VPMG::focusFillBound -- Old mesh maxs = 131.889, 176.043, 140.131 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.410000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.210000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.350000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.731500e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 6.631384e-02 PMG: contraction number = 6.631384e-02 PMG: iteration = 2 PMG: relative residual = 9.402391e-03 PMG: contraction number = 1.417863e-01 PMG: iteration = 3 PMG: relative residual = 2.192358e-03 PMG: contraction number = 2.331702e-01 PMG: iteration = 4 PMG: relative residual = 5.577873e-04 PMG: contraction number = 2.544235e-01 PMG: iteration = 5 PMG: relative residual = 2.783514e-04 PMG: contraction number = 4.990279e-01 PMG: iteration = 6 PMG: relative residual = 8.919519e-05 PMG: contraction number = 3.204410e-01 PMG: iteration = 7 PMG: relative residual = 5.707817e-05 PMG: contraction number = 6.399242e-01 PMG: iteration = 8 PMG: relative residual = 1.852359e-05 PMG: contraction number = 3.245303e-01 PMG: iteration = 9 PMG: relative residual = 1.268784e-05 PMG: contraction number = 6.849559e-01 PMG: iteration = 10 PMG: relative residual = 4.072472e-06 PMG: contraction number = 3.209743e-01 PMG: iteration = 11 PMG: relative residual = 2.868877e-06 PMG: contraction number = 7.044560e-01 PMG: iteration = 12 PMG: relative residual = 9.157592e-07 PMG: contraction number = 3.192047e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.189400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.292700e+02 Vpmg_setPart: lower corner = (-81.671, -42.192, -71.667) Vpmg_setPart: upper corner = (89.114, 132.056, 97.813) Vpmg_setPart: actual minima = (-81.671, -42.192, -71.667) Vpmg_setPart: actual maxima = (89.114, 132.056, 97.813) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.022700e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:40:02 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 10:40:52 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:18:53 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:19:03 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... Vpmg_fillco: done filling coefficient arrays PBEparm_parseToken: trying chgm... Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.970000e+00 NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... Vnm_tstart: starting timer 28 (Solver timer).. NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.220000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126000e+01 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 PMG: contraction number = 1.000000e+00 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 PMG: relative residual = 9.203867e-02 PMG: contraction number = 9.203867e-02 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... PMG: iteration = 2 PMG: relative residual = 1.235397e-02 PMG: contraction number = 1.342258e-01 PMG: iteration = 3 PMG: relative residual = 3.251515e-03 PMG: contraction number = 2.631961e-01 PMG: iteration = 4 PMG: relative residual = 7.779779e-04 PMG: contraction number = 2.392663e-01 PMG: iteration = 5 PMG: relative residual = 3.709536e-04 PMG: contraction number = 4.768176e-01 PMG: iteration = 6 PMG: relative residual = 1.138415e-04 PMG: contraction number = 3.068888e-01 Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.300000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. PMG: iteration = 7 PMG: relative residual = 6.299381e-05 PMG: contraction number = 5.533465e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 6.400000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. PMG: iteration = 8 PMG: relative residual = 2.054304e-05 PMG: contraction number = 3.261120e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.110000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 9 PMG: relative residual = 1.143048e-05 PMG: contraction number = 5.564160e-01 PMG: iteration = 1 PMG: relative residual = 9.484859e-02 PMG: contraction number = 9.484859e-02 PMG: iteration = 10 PMG: relative residual = 3.821412e-06 PMG: contraction number = 3.343179e-01 PMG: iteration = 2 PMG: relative residual = 1.387728e-02 PMG: contraction number = 1.463099e-01 PMG: iteration = 11 PMG: relative residual = 2.099596e-06 PMG: contraction number = 5.494294e-01 PMG: iteration = 3 PMG: relative residual = 5.025394e-03 PMG: contraction number = 3.621310e-01 PMG: iteration = 12 PMG: relative residual = 7.132159e-07 PMG: contraction number = 3.396919e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.229000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.549000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 PMG: iteration = 4 timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 PMG: relative residual = 1.701954e-03 Vnm_tstart: starting timer 27 (Setup timer).. PMG: contraction number = 3.386707e-01 Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 PMG: iteration = 5 Vpbe_ctor2: zmagic = 6773.76 PMG: relative residual = 1.086154e-03 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table PMG: contraction number = 6.381808e-01 Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! PMG: iteration = 6 VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 PMG: relative residual = 4.919519e-04 PMG: contraction number = 4.529301e-01 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... PMG: iteration = 7 PMG: relative residual = 3.165704e-04 PMG: contraction number = 6.434987e-01 PMG: iteration = 8 PMG: relative residual = 1.551670e-04 PMG: contraction number = 4.901500e-01 PMG: iteration = 9 PMG: relative residual = 9.641661e-05 PMG: contraction number = 6.213732e-01 PMG: iteration = 10 PMG: relative residual = 4.890153e-05 PMG: contraction number = 5.071899e-01 PMG: iteration = 11 PMG: relative residual = 2.974743e-05 PMG: contraction number = 6.083128e-01 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.510000e+00 PMG: iteration = 12 timer 28 (Solver timer).. PMG: relative residual = 1.534917e-05 PMG: contraction number = 5.159832e-01 Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 6.200000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. PMG: iteration = 13 PMG: relative residual = 9.227034e-06 PMG: contraction number = 6.011421e-01 PMG: iteration = 14 PMG: relative residual = 4.804737e-06 PMG: contraction number = 5.207238e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.100000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.732000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 15 PMG: relative residual = 2.869176e-06 PMG: contraction number = 5.971557e-01 PMG: iteration = 1 PMG: relative residual = 1.296044e-01 PMG: contraction number = 1.296044e-01 PMG: iteration = 16 PMG: relative residual = 1.501602e-06 PMG: contraction number = 5.233567e-01 PMG: iteration = 2 PMG: relative residual = 1.752819e-02 PMG: contraction number = 1.352438e-01 PMG: iteration = 3 PMG: relative residual = 3.141082e-03 PMG: contraction number = 1.792017e-01 PMG: iteration = 4 PMG: relative residual = 6.355540e-04 PMG: contraction number = 2.023360e-01 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:20:07 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:20:28 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:20:46 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.900000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.100000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.450000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.203867e-02 PMG: contraction number = 9.203867e-02 PMG: iteration = 2 PMG: relative residual = 1.235397e-02 PMG: contraction number = 1.342258e-01 PMG: iteration = 3 PMG: relative residual = 3.251515e-03 PMG: contraction number = 2.631961e-01 PMG: iteration = 4 PMG: relative residual = 7.779779e-04 PMG: contraction number = 2.392663e-01 PMG: iteration = 5 PMG: relative residual = 3.709536e-04 PMG: contraction number = 4.768176e-01 PMG: iteration = 6 PMG: relative residual = 1.138415e-04 PMG: contraction number = 3.068888e-01 PMG: iteration = 7 PMG: relative residual = 6.299381e-05 PMG: contraction number = 5.533465e-01 PMG: iteration = 8 PMG: relative residual = 2.054304e-05 PMG: contraction number = 3.261120e-01 PMG: iteration = 9 PMG: relative residual = 1.143048e-05 PMG: contraction number = 5.564160e-01 PMG: iteration = 10 PMG: relative residual = 3.821412e-06 PMG: contraction number = 3.343179e-01 PMG: iteration = 11 PMG: relative residual = 2.099596e-06 PMG: contraction number = 5.494294e-01 PMG: iteration = 12 PMG: relative residual = 7.132159e-07 PMG: contraction number = 3.396919e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.384000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.732000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (72.879, 88.632, 73.734) Vclist_setupGrid: Grid lower corner = (6.755, 7.731, 6.892) Vclist_assignAtoms: Have 6776005 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.930000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.200000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.810000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.805000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.296044e-01 PMG: contraction number = 1.296044e-01 PMG: iteration = 2 PMG: relative residual = 1.752819e-02 PMG: contraction number = 1.352438e-01 PMG: iteration = 3 PMG: relative residual = 3.141082e-03 PMG: contraction number = 1.792017e-01 PMG: iteration = 4 PMG: relative residual = 6.355540e-04 PMG: contraction number = 2.023360e-01 PMG: iteration = 5 PMG: relative residual = 1.921930e-04 PMG: contraction number = 3.024023e-01 PMG: iteration = 6 PMG: relative residual = 5.883113e-05 PMG: contraction number = 3.061045e-01 PMG: iteration = 7 PMG: relative residual = 2.591838e-05 PMG: contraction number = 4.405555e-01 PMG: iteration = 8 PMG: relative residual = 1.037723e-05 PMG: contraction number = 4.003812e-01 PMG: iteration = 9 PMG: relative residual = 5.068662e-06 PMG: contraction number = 4.884407e-01 PMG: iteration = 10 PMG: relative residual = 2.337104e-06 PMG: contraction number = 4.610890e-01 PMG: iteration = 11 PMG: relative residual = 1.140685e-06 PMG: contraction number = 4.880764e-01 PMG: iteration = 12 PMG: relative residual = 5.642622e-07 PMG: contraction number = 4.946694e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.345000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.727000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.358700e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:23:05 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 11:23:40 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.220000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.560000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.484859e-02 PMG: contraction number = 9.484859e-02 PMG: iteration = 2 PMG: relative residual = 1.387728e-02 PMG: contraction number = 1.463099e-01 PMG: iteration = 3 PMG: relative residual = 5.025394e-03 PMG: contraction number = 3.621310e-01 PMG: iteration = 4 PMG: relative residual = 1.701954e-03 PMG: contraction number = 3.386707e-01 PMG: iteration = 5 PMG: relative residual = 1.086154e-03 PMG: contraction number = 6.381808e-01 PMG: iteration = 6 PMG: relative residual = 4.919519e-04 PMG: contraction number = 4.529301e-01 PMG: iteration = 7 PMG: relative residual = 3.165704e-04 PMG: contraction number = 6.434987e-01 PMG: iteration = 8 PMG: relative residual = 1.551670e-04 PMG: contraction number = 4.901500e-01 PMG: iteration = 9 PMG: relative residual = 9.641661e-05 PMG: contraction number = 6.213732e-01 PMG: iteration = 10 PMG: relative residual = 4.890153e-05 PMG: contraction number = 5.071899e-01 PMG: iteration = 11 PMG: relative residual = 2.974743e-05 PMG: contraction number = 6.083128e-01 PMG: iteration = 12 PMG: relative residual = 1.534917e-05 PMG: contraction number = 5.159832e-01 PMG: iteration = 13 PMG: relative residual = 9.227034e-06 PMG: contraction number = 6.011421e-01 PMG: iteration = 14 PMG: relative residual = 4.804737e-06 PMG: contraction number = 5.207238e-01 PMG: iteration = 15 PMG: relative residual = 2.869176e-06 PMG: contraction number = 5.971557e-01 PMG: iteration = 16 PMG: relative residual = 1.501602e-06 PMG: contraction number = 5.233567e-01 PMG: iteration = 17 PMG: relative residual = 8.933127e-07 PMG: contraction number = 5.949064e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 7.329000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.689000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.760000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 5.200000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.520000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.760000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.308403e-01 PMG: contraction number = 1.308403e-01 PMG: iteration = 2 PMG: relative residual = 1.798493e-02 PMG: contraction number = 1.374571e-01 PMG: iteration = 3 PMG: relative residual = 3.998841e-03 PMG: contraction number = 2.223440e-01 PMG: iteration = 4 PMG: relative residual = 1.208122e-03 PMG: contraction number = 3.021181e-01 PMG: iteration = 5 PMG: relative residual = 6.757788e-04 PMG: contraction number = 5.593629e-01 PMG: iteration = 6 PMG: relative residual = 3.359785e-04 PMG: contraction number = 4.971723e-01 PMG: iteration = 7 PMG: relative residual = 2.245786e-04 PMG: contraction number = 6.684315e-01 PMG: iteration = 8 PMG: relative residual = 1.218076e-04 PMG: contraction number = 5.423831e-01 PMG: iteration = 9 PMG: relative residual = 8.054516e-05 PMG: contraction number = 6.612490e-01 PMG: iteration = 10 PMG: relative residual = 4.482449e-05 PMG: contraction number = 5.565138e-01 PMG: iteration = 11 PMG: relative residual = 2.923878e-05 PMG: contraction number = 6.522948e-01 PMG: iteration = 12 PMG: relative residual = 1.647713e-05 PMG: contraction number = 5.635367e-01 PMG: iteration = 13 PMG: relative residual = 1.065689e-05 PMG: contraction number = 6.467688e-01 PMG: iteration = 14 PMG: relative residual = 6.049021e-06 PMG: contraction number = 5.676159e-01 PMG: iteration = 15 PMG: relative residual = 3.891927e-06 PMG: contraction number = 6.433979e-01 PMG: iteration = 16 PMG: relative residual = 2.218809e-06 PMG: contraction number = 5.701055e-01 PMG: iteration = 17 PMG: relative residual = 1.422917e-06 PMG: contraction number = 6.412978e-01 PMG: iteration = 18 PMG: relative residual = 8.134154e-07 PMG: contraction number = 5.716533e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 8.039000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.379000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.823600e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:08:40 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:08:57 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/129_last_frame_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:09:01 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (86.047, 53.287, 30.58) Valist_getStatistics: Min atom coordinate: (11.099, -15.64, -44.327) Valist_getStatistics: Molecule center: (48.573, 18.8235, -6.8735) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.688394, 0.633312, 0.689802 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.509104, 0.476703, 0.509932 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.739554, 0.752715, 0.739245 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 114.759 79.6214 59.3475 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -17.4128 -41.9745 -73.0944 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.170000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.700000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.610000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 8.368343e-02 PMG: contraction number = 8.368343e-02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:09:18 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/116_last_frame_chainC.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe PMG: iteration = 2 NOsh_parseMG: Parsing bcfl... PMG: relative residual = 1.069266e-02 PMG: contraction number = 1.277752e-01 PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PMG: iteration = 3 trying write... PMG: relative residual = 1.678256e-03 PMG: contraction number = 1.569540e-01 MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (160.328, 151.246, 207.786) Valist_getStatistics: Min atom coordinate: (84.013, 83.637, 136.457) Valist_getStatistics: Molecule center: (122.171, 117.442, 172.121) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.697009, 0.621642, 0.656351 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.514172, 0.469839, 0.490255 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.737683, 0.755802, 0.746941 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 188.986 177.119 235.231 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = 55.1606 57.7639 109.212 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 171.434 162.546 219.286 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 72.713 72.337 125.157 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 171.434 162.546 219.286 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 72.713 72.337 125.157 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 47.3654 Vpbe_ctor2: solute dimensions = 78.721 x 70.209 x 74.129 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. PMG: relative residual = 2.981480e-04 PMG: contraction number = 1.776534e-01 Vclist_setupGrid: Grid lengths = (88.527, 79.821, 83.541) Vclist_setupGrid: Grid lower corner = (77.907, 77.531, 130.351) Vclist_assignAtoms: Have 5711348 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... PMG: iteration = 5 PMG: relative residual = 6.638306e-05 PMG: contraction number = 2.226514e-01 PMG: iteration = 6 PMG: relative residual = 1.969744e-05 PMG: contraction number = 2.967240e-01 PMG: iteration = 7 PMG: relative residual = 6.685430e-06 PMG: contraction number = 3.394060e-01 PMG: iteration = 8 PMG: relative residual = 2.171219e-06 PMG: contraction number = 3.247688e-01 Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.032000e+01 Vnm_tstart: starting timer 28 (Solver timer).. PMG: iteration = 9 PMG: relative residual = 7.374549e-07 PMG: contraction number = 3.396502e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.537000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.928000e+01 Vpmg_setPart: lower corner = (-17.4128, -41.9745, -73.0944) Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. 3475) Vpmg_setPart: actual minima = (-17.4128, -41.9745, -73.0944) Vpmg_setPart: actual maxima = (114.759, 79.6214, 59.3475) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -0.201, -26.94, -55.827 VPMG::focusFillBound -- New mesh maxs = 97.547, 64.587, 42.08 VPMG::focusFillBound -- Old mesh mins = -17.4128, -41.9745, -73.0944 VPMG::focusFillBound -- Old mesh maxs = 114.759, 79.6214, 59.3475 Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.130000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.240000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... PMG: iteration = 1 PMG: relative residual = 8.795004e-02 PMG: contraction number = 8.795004e-02 PMG: iteration = 2 PMG: relative residual = 1.146796e-02 PMG: contraction number = 1.303918e-01 PMG: iteration = 3 PMG: relative residual = 1.836736e-03 PMG: contraction number = 1.601624e-01 PMG: iteration = 4 PMG: relative residual = 3.315982e-04 PMG: contraction number = 1.805366e-01 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.147000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. PMG: iteration = 5 PMG: relative residual = 6.922074e-05 PMG: contraction number = 2.087489e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.090000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. PMG: iteration = 6 PMG: relative residual = 1.814178e-05 PMG: contraction number = 2.620860e-01 PMG: iteration = 7 PMG: relative residual = 5.523662e-06 PMG: contraction number = 3.044718e-01 PMG: iteration = 8 PMG: relative residual = 1.815383e-06 PMG: contraction number = 3.286556e-01 PMG: iteration = 9 PMG: relative residual = 5.975854e-07 PMG: contraction number = 3.291788e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.627000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.037000e+01 Vpmg_setPart: lower corner = (55.1606, 57.7639, 109.212) Vpmg_setPart: upper corner = (188.986, 177.119, 235.231) Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.140000e+00 Vpmg_setPart: actual minima = (55.1606, 57.7639, 109.212) Vpmg_setPart: actual maxima = (188.986, 177.119, 235.231) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.578000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 47.3654 Vpbe_ctor2: solute dimensions = 78.721 x 70.209 x 74.129 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (88.527, 79.821, 83.541) Vclist_setupGrid: Grid lower corner = (77.907, 77.531, 130.351) Vclist_assignAtoms: Have 5711348 atom entries PMG: iteration = 1 PMG: relative residual = 1.327222e-01 PMG: contraction number = 1.327222e-01 Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 72.713, 72.337, 125.157 VPMG::focusFillBound -- New mesh maxs = 171.434, 162.546, 219.286 VPMG::focusFillBound -- Old mesh mins = 55.1606, 57.7639, 109.212 VPMG::focusFillBound -- Old mesh maxs = 188.986, 177.119, 235.231 PMG: iteration = 2 PMG: relative residual = 1.794935e-02 PMG: contraction number = 1.352401e-01 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... PMG: iteration = 3 PMG: relative residual = 2.901301e-03 PMG: contraction number = 1.616382e-01 PMG: iteration = 4 PMG: relative residual = 5.625004e-04 PMG: contraction number = 1.938787e-01 PMG: iteration = 5 PMG: relative residual = 1.538090e-04 PMG: contraction number = 2.734381e-01 PMG: iteration = 6 PMG: relative residual = 4.564919e-05 PMG: contraction number = 2.967914e-01 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.241000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. PMG: iteration = 7 PMG: relative residual = 1.770282e-05 PMG: contraction number = 3.878013e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 9.500000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.760000e+00 PMG: iteration = 8 PMG: relative residual = 6.523346e-06 PMG: contraction number = 3.684919e-01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.824000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: iteration = 9 ber = 1.000000e+00 PMG: relative residual = 2.730516e-06 PMG: contraction number = 4.185760e-01 PMG: iteration = 1 PMG: relative residual = 1.356604e-01 PMG: contraction number = 1.356604e-01 PMG: iteration = 10 PMG: relative residual = 1.053363e-06 PMG: contraction number = 3.857743e-01 PMG: iteration = 2 PMG: relative residual = 1.860176e-02 PMG: contraction number = 1.371200e-01 PMG: iteration = 11 PMG: relative residual = 4.417477e-07 PMG: contraction number = 4.193690e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.878000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.440000e+01 Vpmg_setPart: lower corner = (-0.201, -26.94, -55.827) Vpmg_setPart: upper corner = (97.547, 64.587, 42.08) Vpmg_setPart: actual minima = (-0.201, -26.94, -55.827) Vpmg_setPart: actual maxima = (97.547, 64.587, 42.08) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 PMG: iteration = 3 PMG: relative residual = 2.993771e-03 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. PMG: iteration = 4 PMG: relative residual = 5.520109e-04 PMG: contraction number = 1.843865e-01 PMG: iteration = 5 PMG: relative residual = 1.219640e-04 PMG: contraction number = 2.209449e-01 PMG: iteration = 6 PMG: relative residual = 3.256147e-05 PMG: contraction number = 2.669761e-01 PMG: iteration = 7 PMG: relative residual = 9.514647e-06 PMG: contraction number = 2.922057e-01 PMG: iteration = 8 PMG: relative residual = 3.266249e-06 PMG: contraction number = 3.432864e-01 PMG: iteration = 9 PMG: relative residual = 1.101260e-06 PMG: contraction number = 3.371636e-01 PMG: iteration = 10 PMG: relative residual = 4.136529e-07 PMG: contraction number = 3.756178e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.044000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.537000e+01 Vpmg_setPart: lower corner = (72.713, 72.337, 125.157) Vpmg_setPart: upper corner = (171.434, 162.546, 219.286) Vpmg_setPart: actual minima = (72.713, 72.337, 125.157) Vpmg_setPart: actual maxima = (171.434, 162.546, 219.286) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.623400e+02 Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.551700e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:12:48 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/129_last_frame_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (86.047, 53.287, 30.58) Valist_getStatistics: Min atom coordinate: (11.099, -15.64, -44.327) Valist_getStatistics: Molecule center: (48.573, 18.8235, -6.8735) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.688394, 0.633312, 0.689802 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.509104, 0.476703, 0.509932 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.739554, 0.752715, 0.739245 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 114.759 79.6214 59.3475 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -17.4128 -41.9745 -73.0944 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.330000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 8.100000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 1.940000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.279000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 8.368343e-02 PMG: contraction number = 8.368343e-02 PMG: iteration = 2 PMG: relative residual = 1.069266e-02 PMG: contraction number = 1.277752e-01 PMG: iteration = 3 PMG: relative residual = 1.678256e-03 PMG: contraction number = 1.569540e-01 PMG: iteration = 4 PMG: relative residual = 2.981480e-04 PMG: contraction number = 1.776534e-01 PMG: iteration = 5 PMG: relative residual = 6.638306e-05 PMG: contraction number = 2.226514e-01 PMG: iteration = 6 PMG: relative residual = 1.969744e-05 PMG: contraction number = 2.967240e-01 PMG: iteration = 7 PMG: relative residual = 6.685430e-06 PMG: contraction number = 3.394060e-01 PMG: iteration = 8 PMG: relative residual = 2.171219e-06 PMG: contraction number = 3.247688e-01 PMG: iteration = 9 PMG: relative residual = 7.374549e-07 PMG: contraction number = 3.396502e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.766000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.108000e+01 Vpmg_setPart: lower corner = (-17.4128, -41.9745, -73.0944) Vpmg_setPart: upper corner = (114.759, 79.6214, 59.3475) Vpmg_setPart: actual minima = (-17.4128, -41.9745, -73.0944) Vpmg_setPart: actual maxima = (114.759, 79.6214, 59.3475) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -0.201, -26.94, -55.827 VPMG::focusFillBound -- New mesh maxs = 97.547, 64.587, 42.08 VPMG::focusFillBound -- Old mesh mins = -17.4128, -41.9745, -73.0944 VPMG::focusFillBound -- Old mesh maxs = 114.759, 79.6214, 59.3475 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.061000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.700000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.370000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.503000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.327222e-01 PMG: contraction number = 1.327222e-01 PMG: iteration = 2 PMG: relative residual = 1.794935e-02 PMG: contraction number = 1.352401e-01 PMG: iteration = 3 PMG: relative residual = 2.901301e-03 PMG: contraction number = 1.616382e-01 PMG: iteration = 4 PMG: relative residual = 5.625004e-04 PMG: contraction number = 1.938787e-01 PMG: iteration = 5 PMG: relative residual = 1.538090e-04 PMG: contraction number = 2.734381e-01 PMG: iteration = 6 PMG: relative residual = 4.564919e-05 PMG: contraction number = 2.967914e-01 PMG: iteration = 7 PMG: relative residual = 1.770282e-05 PMG: contraction number = 3.878013e-01 PMG: iteration = 8 PMG: relative residual = 6.523346e-06 PMG: contraction number = 3.684919e-01 PMG: iteration = 9 PMG: relative residual = 2.730516e-06 PMG: contraction number = 4.185760e-01 PMG: iteration = 10 PMG: relative residual = 1.053363e-06 PMG: contraction number = 3.857743e-01 PMG: iteration = 11 PMG: relative residual = 4.417477e-07 PMG: contraction number = 4.193690e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.944000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.315000e+01 Vpmg_setPart: lower corner = (-0.201, -26.94, -55.827) Vpmg_setPart: upper corner = (97.547, 64.587, 42.08) Vpmg_setPart: actual minima = (-0.201, -26.94, -55.827) Vpmg_setPart: actual maxima = (97.547, 64.587, 42.08) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.608700e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:14:53 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:15:21 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/129_last_frame_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (86.047, 53.287, 30.58) Valist_getStatistics: Min atom coordinate: (11.099, -15.64, -44.327) Valist_getStatistics: Molecule center: (48.573, 18.8235, -6.8735) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.688394, 0.633312, 0.689802 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.509104, 0.476703, 0.509932 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.739554, 0.752715, 0.739245 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 48.673 18.8235 -6.8735 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 114.759 79.6214 59.3475 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -17.4128 -41.9745 -73.0944 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 97.547 64.587 42.08 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -0.201 -26.94 -55.827 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.290000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 8.000000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.030000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 8.368343e-02 PMG: contraction number = 8.368343e-02 PMG: iteration = 2 PMG: relative residual = 1.069266e-02 PMG: contraction number = 1.277752e-01 PMG: iteration = 3 PMG: relative residual = 1.678256e-03 PMG: contraction number = 1.569540e-01 PMG: iteration = 4 PMG: relative residual = 2.981480e-04 PMG: contraction number = 1.776534e-01 PMG: iteration = 5 PMG: relative residual = 6.638306e-05 PMG: contraction number = 2.226514e-01 PMG: iteration = 6 PMG: relative residual = 1.969744e-05 PMG: contraction number = 2.967240e-01 PMG: iteration = 7 PMG: relative residual = 6.685430e-06 PMG: contraction number = 3.394060e-01 PMG: iteration = 8 PMG: relative residual = 2.171219e-06 PMG: contraction number = 3.247688e-01 PMG: iteration = 9 PMG: relative residual = 7.374549e-07 PMG: contraction number = 3.396502e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.308000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.702000e+01 Vpmg_setPart: lower corner = (-17.4128, -41.9745, -73.0944) Vpmg_setPart: upper corner = (114.759, 79.6214, 59.3475) Vpmg_setPart: actual minima = (-17.4128, -41.9745, -73.0944) Vpmg_setPart: actual maxima = (114.759, 79.6214, 59.3475) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 45.6791 Vpbe_ctor2: solute dimensions = 77.748 x 71.527 x 77.907 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (87.302, 81.281, 87.261) Vclist_setupGrid: Grid lower corner = (4.922, -21.817, -50.504) Vclist_assignAtoms: Have 5534664 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -0.201, -26.94, -55.827 VPMG::focusFillBound -- New mesh maxs = 97.547, 64.587, 42.08 VPMG::focusFillBound -- Old mesh mins = -17.4128, -41.9745, -73.0944 VPMG::focusFillBound -- Old mesh maxs = 114.759, 79.6214, 59.3475 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.077000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.900000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.220000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.083000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.327222e-01 PMG: contraction number = 1.327222e-01 PMG: iteration = 2 PMG: relative residual = 1.794935e-02 PMG: contraction number = 1.352401e-01 PMG: iteration = 3 PMG: relative residual = 2.901301e-03 PMG: contraction number = 1.616382e-01 PMG: iteration = 4 PMG: relative residual = 5.625004e-04 PMG: contraction number = 1.938787e-01 PMG: iteration = 5 PMG: relative residual = 1.538090e-04 PMG: contraction number = 2.734381e-01 PMG: iteration = 6 PMG: relative residual = 4.564919e-05 PMG: contraction number = 2.967914e-01 PMG: iteration = 7 PMG: relative residual = 1.770282e-05 PMG: contraction number = 3.878013e-01 PMG: iteration = 8 PMG: relative residual = 6.523346e-06 PMG: contraction number = 3.684919e-01 PMG: iteration = 9 PMG: relative residual = 2.730516e-06 PMG: contraction number = 4.185760e-01 PMG: iteration = 10 PMG: relative residual = 1.053363e-06 PMG: contraction number = 3.857743e-01 PMG: iteration = 11 PMG: relative residual = 4.417477e-07 PMG: contraction number = 4.193690e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.904000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.256000e+01 Vpmg_setPart: lower corner = (-0.201, -26.94, -55.827) Vpmg_setPart: upper corner = (97.547, 64.587, 42.08) Vpmg_setPart: actual minima = (-0.201, -26.94, -55.827) Vpmg_setPart: actual maxima = (97.547, 64.587, 42.08) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.560000e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:29:31 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:29:39 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/116_last_frame_chainC.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (160.328, 151.246, 207.786) Valist_getStatistics: Min atom coordinate: (84.013, 83.637, 136.457) Valist_getStatistics: Molecule center: (122.171, 117.442, 172.121) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.697009, 0.621642, 0.656351 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.514172, 0.469839, 0.490255 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.737683, 0.755802, 0.746941 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 122.073 117.442 172.221 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 188.986 177.119 235.231 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = 55.1606 57.7639 109.212 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 171.434 162.546 219.286 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 72.713 72.337 125.157 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 171.434 162.546 219.286 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 72.713 72.337 125.157 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 47.3654 Vpbe_ctor2: solute dimensions = 78.721 x 70.209 x 74.129 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (88.527, 79.821, 83.541) Vclist_setupGrid: Grid lower corner = (77.907, 77.531, 130.351) Vclist_assignAtoms: Have 5711348 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.300000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.500000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.380000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 8.795004e-02 PMG: contraction number = 8.795004e-02 PMG: iteration = 2 PMG: relative residual = 1.146796e-02 PMG: contraction number = 1.303918e-01 PMG: iteration = 3 PMG: relative residual = 1.836736e-03 PMG: contraction number = 1.601624e-01 PMG: iteration = 4 PMG: relative residual = 3.315982e-04 PMG: contraction number = 1.805366e-01 PMG: iteration = 5 PMG: relative residual = 6.922074e-05 PMG: contraction number = 2.087489e-01 PMG: iteration = 6 PMG: relative residual = 1.814178e-05 PMG: contraction number = 2.620860e-01 PMG: iteration = 7 PMG: relative residual = 5.523662e-06 PMG: contraction number = 3.044718e-01 PMG: iteration = 8 PMG: relative residual = 1.815383e-06 PMG: contraction number = 3.286556e-01 PMG: iteration = 9 PMG: relative residual = 5.975854e-07 PMG: contraction number = 3.291788e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.764000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.125000e+01 Vpmg_setPart: lower corner = (55.1606, 57.7639, 109.212) Vpmg_setPart: upper corner = (188.986, 177.119, 235.231) Vpmg_setPart: actual minima = (55.1606, 57.7639, 109.212) Vpmg_setPart: actual maxima = (188.986, 177.119, 235.231) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 47.3654 Vpbe_ctor2: solute dimensions = 78.721 x 70.209 x 74.129 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (88.527, 79.821, 83.541) Vclist_setupGrid: Grid lower corner = (77.907, 77.531, 130.351) Vclist_assignAtoms: Have 5711348 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 193, ny = 193, nz = 193 Vpmg_ctor2: PMG chose nlev = 5 Vpmg_ctor2: PMG chose nxc = 13, nyc = 13, nzc = 13 Vpmg_ctor2: PMG chose nf = 7189057, nc = 2197 Vpmg_ctor2: PMG chose narr = 8237201, narrc = 1048144 Vpmg_ctor2: PMG chose n_rpc = 600, n_iz = 300, n_ipc = 600 Vpmg_ctor2: PMG chose nrwk = 88383488, niwk = 900 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 72.713, 72.337, 125.157 VPMG::focusFillBound -- New mesh maxs = 171.434, 162.546, 219.286 VPMG::focusFillBound -- Old mesh mins = 55.1606, 57.7639, 109.212 VPMG::focusFillBound -- Old mesh maxs = 188.986, 177.119, 235.231 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.067000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 8.400000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.220000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.500000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.356604e-01 PMG: contraction number = 1.356604e-01 PMG: iteration = 2 PMG: relative residual = 1.860176e-02 PMG: contraction number = 1.371200e-01 PMG: iteration = 3 PMG: relative residual = 2.993771e-03 PMG: contraction number = 1.609402e-01 PMG: iteration = 4 PMG: relative residual = 5.520109e-04 PMG: contraction number = 1.843865e-01 PMG: iteration = 5 PMG: relative residual = 1.219640e-04 PMG: contraction number = 2.209449e-01 PMG: iteration = 6 PMG: relative residual = 3.256147e-05 PMG: contraction number = 2.669761e-01 PMG: iteration = 7 PMG: relative residual = 9.514647e-06 PMG: contraction number = 2.922057e-01 PMG: iteration = 8 PMG: relative residual = 3.266249e-06 PMG: contraction number = 3.432864e-01 PMG: iteration = 9 PMG: relative residual = 1.101260e-06 PMG: contraction number = 3.371636e-01 PMG: iteration = 10 PMG: relative residual = 4.136529e-07 PMG: contraction number = 3.756178e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.234000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.590000e+01 Vpmg_setPart: lower corner = (72.713, 72.337, 125.157) Vpmg_setPart: upper corner = (171.434, 162.546, 219.286) Vpmg_setPart: actual minima = (72.713, 72.337, 125.157) Vpmg_setPart: actual maxima = (171.434, 162.546, 219.286) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.536200e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:49:49 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:51:48 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:51:55 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1SVT_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (65.316, -11.944, 5.634) Valist_getStatistics: Min atom coordinate: (7.527, -78.427, -86.134) Valist_getStatistics: Molecule center: (36.4215, -45.1855, -40.25) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.643758, 0.705916, 0.717704 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.503681, 0.519411, 0.511464 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.782408, 0.735798, 0.71264 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 87.8221 27.9044 40.2328 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -15.1791 -107.631 -120.533 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.190000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.400000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.090000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.365000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.007221e-01 PMG: contraction number = 1.007221e-01 PMG: iteration = 2 PMG: relative residual = 1.501112e-02 PMG: contraction number = 1.490350e-01 PMG: iteration = 3 PMG: relative residual = 4.588270e-03 PMG: contraction number = 3.056581e-01 PMG: iteration = 4 PMG: relative residual = 1.734084e-03 PMG: contraction number = 3.779386e-01 PMG: iteration = 5 PMG: relative residual = 1.148349e-03 PMG: contraction number = 6.622225e-01 PMG: iteration = 6 PMG: relative residual = 6.253221e-04 PMG: contraction number = 5.445399e-01 PMG: iteration = 7 PMG: relative residual = 4.595871e-04 PMG: contraction number = 7.349607e-01 PMG: iteration = 8 PMG: relative residual = 2.626687e-04 PMG: contraction number = 5.715320e-01 PMG: iteration = 9 PMG: relative residual = 1.922997e-04 PMG: contraction number = 7.320998e-01 PMG: iteration = 10 PMG: relative residual = 1.114188e-04 PMG: contraction number = 5.794019e-01 PMG: iteration = 11 PMG: relative residual = 8.105634e-05 PMG: contraction number = 7.274922e-01 PMG: iteration = 12 PMG: relative residual = 4.727237e-05 PMG: contraction number = 5.832039e-01 PMG: iteration = 13 PMG: relative residual = 3.424975e-05 PMG: contraction number = 7.245194e-01 PMG: iteration = 14 PMG: relative residual = 2.004573e-05 PMG: contraction number = 5.852811e-01 PMG: iteration = 15 PMG: relative residual = 1.448818e-05 PMG: contraction number = 7.227564e-01 PMG: iteration = 16 PMG: relative residual = 8.496543e-06 PMG: contraction number = 5.864465e-01 PMG: iteration = 17 PMG: relative residual = 6.132232e-06 PMG: contraction number = 7.217326e-01 PMG: iteration = 18 PMG: relative residual = 3.600272e-06 PMG: contraction number = 5.871063e-01 PMG: iteration = 19 PMG: relative residual = 2.596309e-06 PMG: contraction number = 7.211425e-01 PMG: iteration = 20 PMG: relative residual = 1.525284e-06 PMG: contraction number = 5.874816e-01 PMG: iteration = 21 PMG: relative residual = 1.099429e-06 PMG: contraction number = 7.208027e-01 PMG: iteration = 22 PMG: relative residual = 6.461294e-07 PMG: contraction number = 5.876955e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.332500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.376400e+02 Vpmg_setPart: lower corner = (-15.1791, -107.631, -120.533) Vpmg_setPart: upper corner = (87.8221, 27.9044, 40.2328) Vpmg_setPart: actual minima = (-15.1791, -107.631, -120.533) Vpmg_setPart: actual maxima = (87.8221, 27.9044, 40.2328) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -3.973, -89.727, -97.434 VPMG::focusFillBound -- New mesh maxs = 76.616, 10, 17.134 VPMG::focusFillBound -- Old mesh mins = -15.1791, -107.631, -120.533 VPMG::focusFillBound -- Old mesh maxs = 87.8221, 27.9044, 40.2328 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.004000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.090000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.614000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.403849e-01 PMG: contraction number = 1.403849e-01 PMG: iteration = 2 PMG: relative residual = 1.991702e-02 PMG: contraction number = 1.418744e-01 PMG: iteration = 3 PMG: relative residual = 4.686472e-03 PMG: contraction number = 2.352999e-01 PMG: iteration = 4 PMG: relative residual = 1.433610e-03 PMG: contraction number = 3.059038e-01 PMG: iteration = 5 PMG: relative residual = 7.934276e-04 PMG: contraction number = 5.534474e-01 PMG: iteration = 6 PMG: relative residual = 3.881595e-04 PMG: contraction number = 4.892186e-01 PMG: iteration = 7 PMG: relative residual = 2.688394e-04 PMG: contraction number = 6.926004e-01 PMG: iteration = 8 PMG: relative residual = 1.440784e-04 PMG: contraction number = 5.359272e-01 PMG: iteration = 9 PMG: relative residual = 1.022637e-04 PMG: contraction number = 7.097782e-01 PMG: iteration = 10 PMG: relative residual = 5.646177e-05 PMG: contraction number = 5.521194e-01 PMG: iteration = 11 PMG: relative residual = 4.022533e-05 PMG: contraction number = 7.124349e-01 PMG: iteration = 12 PMG: relative residual = 2.256494e-05 PMG: contraction number = 5.609635e-01 PMG: iteration = 13 PMG: relative residual = 1.606807e-05 PMG: contraction number = 7.120813e-01 PMG: iteration = 14 PMG: relative residual = 9.102728e-06 PMG: contraction number = 5.665102e-01 PMG: iteration = 15 PMG: relative residual = 6.469645e-06 PMG: contraction number = 7.107369e-01 PMG: iteration = 16 PMG: relative residual = 3.689088e-06 PMG: contraction number = 5.702150e-01 PMG: iteration = 17 PMG: relative residual = 2.616341e-06 PMG: contraction number = 7.092106e-01 PMG: iteration = 18 PMG: relative residual = 1.498656e-06 PMG: contraction number = 5.728061e-01 PMG: iteration = 19 PMG: relative residual = 1.060746e-06 PMG: contraction number = 7.077983e-01 PMG: iteration = 20 PMG: relative residual = 6.095830e-07 PMG: contraction number = 5.746738e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.216200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.260700e+02 Vpmg_setPart: lower corner = (-3.973, -89.727, -97.434) Vpmg_setPart: upper corner = (76.616, 10, 17.134) Vpmg_setPart: actual minima = (-3.973, -89.727, -97.434) Vpmg_setPart: actual maxima = (76.616, 10, 17.134) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.891500e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:54:52 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Oct 12 17:54:58 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1SVT_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (65.316, -11.944, 5.634) Valist_getStatistics: Min atom coordinate: (7.527, -78.427, -86.134) Valist_getStatistics: Molecule center: (36.4215, -45.1855, -40.25) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.643758, 0.705916, 0.717704 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.503681, 0.519411, 0.511464 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.782408, 0.735798, 0.71264 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 87.8221 27.9044 40.2328 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -15.1791 -107.631 -120.533 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.830000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.380000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.361000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.007221e-01 PMG: contraction number = 1.007221e-01 PMG: iteration = 2 PMG: relative residual = 1.501112e-02 PMG: contraction number = 1.490350e-01 PMG: iteration = 3 PMG: relative residual = 4.588270e-03 PMG: contraction number = 3.056581e-01 PMG: iteration = 4 PMG: relative residual = 1.734084e-03 PMG: contraction number = 3.779386e-01 PMG: iteration = 5 PMG: relative residual = 1.148349e-03 PMG: contraction number = 6.622225e-01 PMG: iteration = 6 PMG: relative residual = 6.253221e-04 PMG: contraction number = 5.445399e-01 PMG: iteration = 7 PMG: relative residual = 4.595871e-04 PMG: contraction number = 7.349607e-01 PMG: iteration = 8 PMG: relative residual = 2.626687e-04 PMG: contraction number = 5.715320e-01 PMG: iteration = 9 PMG: relative residual = 1.922997e-04 PMG: contraction number = 7.320998e-01 PMG: iteration = 10 PMG: relative residual = 1.114188e-04 PMG: contraction number = 5.794019e-01 PMG: iteration = 11 PMG: relative residual = 8.105634e-05 PMG: contraction number = 7.274922e-01 PMG: iteration = 12 PMG: relative residual = 4.727237e-05 PMG: contraction number = 5.832039e-01 PMG: iteration = 13 PMG: relative residual = 3.424975e-05 PMG: contraction number = 7.245194e-01 PMG: iteration = 14 PMG: relative residual = 2.004573e-05 PMG: contraction number = 5.852811e-01 PMG: iteration = 15 PMG: relative residual = 1.448818e-05 PMG: contraction number = 7.227564e-01 PMG: iteration = 16 PMG: relative residual = 8.496543e-06 PMG: contraction number = 5.864465e-01 PMG: iteration = 17 PMG: relative residual = 6.132232e-06 PMG: contraction number = 7.217326e-01 PMG: iteration = 18 PMG: relative residual = 3.600272e-06 PMG: contraction number = 5.871063e-01 PMG: iteration = 19 PMG: relative residual = 2.596309e-06 PMG: contraction number = 7.211425e-01 PMG: iteration = 20 PMG: relative residual = 1.525284e-06 PMG: contraction number = 5.874816e-01 PMG: iteration = 21 PMG: relative residual = 1.099429e-06 PMG: contraction number = 7.208027e-01 PMG: iteration = 22 PMG: relative residual = 6.461294e-07 PMG: contraction number = 5.876955e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.328800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.374900e+02 Vpmg_setPart: lower corner = (-15.1791, -107.631, -120.533) Vpmg_setPart: upper corner = (87.8221, 27.9044, 40.2328) Vpmg_setPart: actual minima = (-15.1791, -107.631, -120.533) Vpmg_setPart: actual maxima = (87.8221, 27.9044, 40.2328) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -3.973, -89.727, -97.434 VPMG::focusFillBound -- New mesh maxs = 76.616, 10, 17.134 VPMG::focusFillBound -- Old mesh mins = -15.1791, -107.631, -120.533 VPMG::focusFillBound -- Old mesh maxs = 87.8221, 27.9044, 40.2328 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.011000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.400000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.700000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.616500e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.403849e-01 PMG: contraction number = 1.403849e-01 PMG: iteration = 2 PMG: relative residual = 1.991702e-02 PMG: contraction number = 1.418744e-01 PMG: iteration = 3 PMG: relative residual = 4.686472e-03 PMG: contraction number = 2.352999e-01 PMG: iteration = 4 PMG: relative residual = 1.433610e-03 PMG: contraction number = 3.059038e-01 PMG: iteration = 5 PMG: relative residual = 7.934276e-04 PMG: contraction number = 5.534474e-01 PMG: iteration = 6 PMG: relative residual = 3.881595e-04 PMG: contraction number = 4.892186e-01 PMG: iteration = 7 PMG: relative residual = 2.688394e-04 PMG: contraction number = 6.926004e-01 PMG: iteration = 8 PMG: relative residual = 1.440784e-04 PMG: contraction number = 5.359272e-01 PMG: iteration = 9 PMG: relative residual = 1.022637e-04 PMG: contraction number = 7.097782e-01 PMG: iteration = 10 PMG: relative residual = 5.646177e-05 PMG: contraction number = 5.521194e-01 PMG: iteration = 11 PMG: relative residual = 4.022533e-05 PMG: contraction number = 7.124349e-01 PMG: iteration = 12 PMG: relative residual = 2.256494e-05 PMG: contraction number = 5.609635e-01 PMG: iteration = 13 PMG: relative residual = 1.606807e-05 PMG: contraction number = 7.120813e-01 PMG: iteration = 14 PMG: relative residual = 9.102728e-06 PMG: contraction number = 5.665102e-01 PMG: iteration = 15 PMG: relative residual = 6.469645e-06 PMG: contraction number = 7.107369e-01 PMG: iteration = 16 PMG: relative residual = 3.689088e-06 PMG: contraction number = 5.702150e-01 PMG: iteration = 17 PMG: relative residual = 2.616341e-06 PMG: contraction number = 7.092106e-01 PMG: iteration = 18 PMG: relative residual = 1.498656e-06 PMG: contraction number = 5.728061e-01 PMG: iteration = 19 PMG: relative residual = 1.060746e-06 PMG: contraction number = 7.077983e-01 PMG: iteration = 20 PMG: relative residual = 6.095830e-07 PMG: contraction number = 5.746738e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.198000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.248900e+02 Vpmg_setPart: lower corner = (-3.973, -89.727, -97.434) Vpmg_setPart: upper corner = (76.616, 10, 17.134) Vpmg_setPart: actual minima = (-3.973, -89.727, -97.434) Vpmg_setPart: actual maxima = (76.616, 10, 17.134) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.877000e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Oct 13 11:21:48 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Oct 13 11:21:57 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1SVT_chainA.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7835 atoms Valist_getStatistics: Max atom coordinate: (65.316, -11.944, 5.634) Valist_getStatistics: Min atom coordinate: (7.527, -78.427, -86.134) Valist_getStatistics: Molecule center: (36.4215, -45.1855, -40.25) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.643758, 0.705916, 0.717704 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.503681, 0.519411, 0.511464 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.782408, 0.735798, 0.71264 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 36.3215 -39.8635 -40.15 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 87.8221 27.9044 40.2328 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -15.1791 -107.631 -120.533 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 76.616 10 17.134 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -3.973 -89.727 -97.434 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.610000e+00 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.300000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.120000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.007221e-01 PMG: contraction number = 1.007221e-01 PMG: iteration = 2 PMG: relative residual = 1.501112e-02 PMG: contraction number = 1.490350e-01 PMG: iteration = 3 PMG: relative residual = 4.588270e-03 PMG: contraction number = 3.056581e-01 PMG: iteration = 4 PMG: relative residual = 1.734084e-03 PMG: contraction number = 3.779386e-01 PMG: iteration = 5 PMG: relative residual = 1.148349e-03 PMG: contraction number = 6.622225e-01 PMG: iteration = 6 PMG: relative residual = 6.253221e-04 PMG: contraction number = 5.445399e-01 PMG: iteration = 7 PMG: relative residual = 4.595871e-04 PMG: contraction number = 7.349607e-01 PMG: iteration = 8 PMG: relative residual = 2.626687e-04 PMG: contraction number = 5.715320e-01 PMG: iteration = 9 PMG: relative residual = 1.922997e-04 PMG: contraction number = 7.320998e-01 PMG: iteration = 10 PMG: relative residual = 1.114188e-04 PMG: contraction number = 5.794019e-01 PMG: iteration = 11 PMG: relative residual = 8.105634e-05 PMG: contraction number = 7.274922e-01 PMG: iteration = 12 PMG: relative residual = 4.727237e-05 PMG: contraction number = 5.832039e-01 PMG: iteration = 13 PMG: relative residual = 3.424975e-05 PMG: contraction number = 7.245194e-01 PMG: iteration = 14 PMG: relative residual = 2.004573e-05 PMG: contraction number = 5.852811e-01 PMG: iteration = 15 PMG: relative residual = 1.448818e-05 PMG: contraction number = 7.227564e-01 PMG: iteration = 16 PMG: relative residual = 8.496543e-06 PMG: contraction number = 5.864465e-01 PMG: iteration = 17 PMG: relative residual = 6.132232e-06 PMG: contraction number = 7.217326e-01 PMG: iteration = 18 PMG: relative residual = 3.600272e-06 PMG: contraction number = 5.871063e-01 PMG: iteration = 19 PMG: relative residual = 2.596309e-06 PMG: contraction number = 7.211425e-01 PMG: iteration = 20 PMG: relative residual = 1.525284e-06 PMG: contraction number = 5.874816e-01 PMG: iteration = 21 PMG: relative residual = 1.099429e-06 PMG: contraction number = 7.208027e-01 PMG: iteration = 22 PMG: relative residual = 6.461294e-07 PMG: contraction number = 5.876955e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.325400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.368800e+02 Vpmg_setPart: lower corner = (-15.1791, -107.631, -120.533) Vpmg_setPart: upper corner = (87.8221, 27.9044, 40.2328) Vpmg_setPart: actual minima = (-15.1791, -107.631, -120.533) Vpmg_setPart: actual maxima = (87.8221, 27.9044, 40.2328) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 51.4037 Vpbe_ctor2: solute dimensions = 60.589 x 69.083 x 94.568 Vpbe_ctor2: solute charge = -17.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (70.001, 78.695, 103.98) Vclist_setupGrid: Grid lower corner = (1.421, -84.533, -92.24) Vclist_assignAtoms: Have 5889316 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 29 Vpmg_ctor2: PMG chose nf = 6991425, nc = 15225 Vpmg_ctor2: PMG chose narr = 8009004, narrc = 1017579 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 91108889, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -3.973, -89.727, -97.434 VPMG::focusFillBound -- New mesh maxs = 76.616, 10, 17.134 VPMG::focusFillBound -- Old mesh mins = -15.1791, -107.631, -120.533 VPMG::focusFillBound -- Old mesh maxs = 87.8221, 27.9044, 40.2328 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.000000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 7.200000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 3.720000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606300e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.403849e-01 PMG: contraction number = 1.403849e-01 PMG: iteration = 2 PMG: relative residual = 1.991702e-02 PMG: contraction number = 1.418744e-01 PMG: iteration = 3 PMG: relative residual = 4.686472e-03 PMG: contraction number = 2.352999e-01 PMG: iteration = 4 PMG: relative residual = 1.433610e-03 PMG: contraction number = 3.059038e-01 PMG: iteration = 5 PMG: relative residual = 7.934276e-04 PMG: contraction number = 5.534474e-01 PMG: iteration = 6 PMG: relative residual = 3.881595e-04 PMG: contraction number = 4.892186e-01 PMG: iteration = 7 PMG: relative residual = 2.688394e-04 PMG: contraction number = 6.926004e-01 PMG: iteration = 8 PMG: relative residual = 1.440784e-04 PMG: contraction number = 5.359272e-01 PMG: iteration = 9 PMG: relative residual = 1.022637e-04 PMG: contraction number = 7.097782e-01 PMG: iteration = 10 PMG: relative residual = 5.646177e-05 PMG: contraction number = 5.521194e-01 PMG: iteration = 11 PMG: relative residual = 4.022533e-05 PMG: contraction number = 7.124349e-01 PMG: iteration = 12 PMG: relative residual = 2.256494e-05 PMG: contraction number = 5.609635e-01 PMG: iteration = 13 PMG: relative residual = 1.606807e-05 PMG: contraction number = 7.120813e-01 PMG: iteration = 14 PMG: relative residual = 9.102728e-06 PMG: contraction number = 5.665102e-01 PMG: iteration = 15 PMG: relative residual = 6.469645e-06 PMG: contraction number = 7.107369e-01 PMG: iteration = 16 PMG: relative residual = 3.689088e-06 PMG: contraction number = 5.702150e-01 PMG: iteration = 17 PMG: relative residual = 2.616341e-06 PMG: contraction number = 7.092106e-01 PMG: iteration = 18 PMG: relative residual = 1.498656e-06 PMG: contraction number = 5.728061e-01 PMG: iteration = 19 PMG: relative residual = 1.060746e-06 PMG: contraction number = 7.077983e-01 PMG: iteration = 20 PMG: relative residual = 6.095830e-07 PMG: contraction number = 5.746738e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.209200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.258500e+02 Vpmg_setPart: lower corner = (-3.973, -89.727, -97.434) Vpmg_setPart: upper corner = (76.616, 10, 17.134) Vpmg_setPart: actual minima = (-3.973, -89.727, -97.434) Vpmg_setPart: actual maxima = (76.616, 10, 17.134) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.874900e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Nov 1 10:11:53 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Nov 1 10:12:04 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.334000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 9.100000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 4.830000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.944000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.126611e-01 PMG: contraction number = 1.126611e-01 PMG: iteration = 2 PMG: relative residual = 1.356183e-02 PMG: contraction number = 1.203773e-01 PMG: iteration = 3 PMG: relative residual = 4.811472e-03 PMG: contraction number = 3.547803e-01 PMG: iteration = 4 PMG: relative residual = 1.624487e-03 PMG: contraction number = 3.376278e-01 PMG: iteration = 5 PMG: relative residual = 1.069524e-03 PMG: contraction number = 6.583764e-01 PMG: iteration = 6 PMG: relative residual = 4.813565e-04 PMG: contraction number = 4.500662e-01 PMG: iteration = 7 PMG: relative residual = 3.106282e-04 PMG: contraction number = 6.453184e-01 PMG: iteration = 8 PMG: relative residual = 1.512342e-04 PMG: contraction number = 4.868657e-01 PMG: iteration = 9 PMG: relative residual = 9.386133e-05 PMG: contraction number = 6.206355e-01 PMG: iteration = 10 PMG: relative residual = 4.735547e-05 PMG: contraction number = 5.045259e-01 PMG: iteration = 11 PMG: relative residual = 2.873169e-05 PMG: contraction number = 6.067239e-01 PMG: iteration = 12 PMG: relative residual = 1.476187e-05 PMG: contraction number = 5.137834e-01 PMG: iteration = 13 PMG: relative residual = 8.844111e-06 PMG: contraction number = 5.991187e-01 PMG: iteration = 14 PMG: relative residual = 4.588341e-06 PMG: contraction number = 5.188018e-01 PMG: iteration = 15 PMG: relative residual = 2.729580e-06 PMG: contraction number = 5.948947e-01 PMG: iteration = 16 PMG: relative residual = 1.423731e-06 PMG: contraction number = 5.215937e-01 PMG: iteration = 17 PMG: relative residual = 8.435855e-07 PMG: contraction number = 5.925173e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 2.739000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.339000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 65201665, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.628000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 9.200000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 4.920000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.931000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.432452e-01 PMG: contraction number = 1.432452e-01 PMG: iteration = 2 PMG: relative residual = 1.616501e-02 PMG: contraction number = 1.128486e-01 PMG: iteration = 3 PMG: relative residual = 3.491778e-03 PMG: contraction number = 2.160084e-01 PMG: iteration = 4 PMG: relative residual = 1.086066e-03 PMG: contraction number = 3.110352e-01 PMG: iteration = 5 PMG: relative residual = 6.579256e-04 PMG: contraction number = 6.057880e-01 PMG: iteration = 6 PMG: relative residual = 3.299878e-04 PMG: contraction number = 5.015579e-01 PMG: iteration = 7 PMG: relative residual = 2.228135e-04 PMG: contraction number = 6.752176e-01 PMG: iteration = 8 PMG: relative residual = 1.203691e-04 PMG: contraction number = 5.402236e-01 PMG: iteration = 9 PMG: relative residual = 7.966699e-05 PMG: contraction number = 6.618557e-01 PMG: iteration = 10 PMG: relative residual = 4.416927e-05 PMG: contraction number = 5.544237e-01 PMG: iteration = 11 PMG: relative residual = 2.877983e-05 PMG: contraction number = 6.515804e-01 PMG: iteration = 12 PMG: relative residual = 1.617540e-05 PMG: contraction number = 5.620396e-01 PMG: iteration = 13 PMG: relative residual = 1.043966e-05 PMG: contraction number = 6.454036e-01 PMG: iteration = 14 PMG: relative residual = 5.914873e-06 PMG: contraction number = 5.665770e-01 PMG: iteration = 15 PMG: relative residual = 3.795077e-06 PMG: contraction number = 6.416159e-01 PMG: iteration = 16 PMG: relative residual = 2.160794e-06 PMG: contraction number = 5.693676e-01 PMG: iteration = 17 PMG: relative residual = 1.381292e-06 PMG: contraction number = 6.392521e-01 PMG: iteration = 18 PMG: relative residual = 7.888654e-07 PMG: contraction number = 5.711069e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 2.904000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.512000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.036800e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Nov 1 14:51:18 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path /home/slars/lutefisk/groel_md/1XCK/analysis/06_electrostatics/1XCK_chainA_MGATP_noWAT.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (161, 193, 161) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 7879 atoms Valist_getStatistics: Max atom coordinate: (73.528, 90.257, 74.52) Valist_getStatistics: Min atom coordinate: (12.861, 13.837, 12.998) Valist_getStatistics: Molecule center: (43.1945, 52.047, 43.759) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.672212, 0.701427, 0.681296 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.520419, 0.516771, 0.525763 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.774189, 0.736742, 0.771709 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 43.1945 51.947 43.759 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 96.9715 119.284 98.2627 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -10.5825 -15.39 -10.7447 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 84.828 101.557 85.82 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.561 2.337 1.698 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 71404397, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoPermanentMultipole... fillcoPermanentMultipole: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.401500e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 8.800000e-01 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.820000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.815512e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.469100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.501626e+05 PMG: contraction number = , 8.501626e+05 NEWTON: attempting damping, relres = 2.174557e-01 NEWTON: attempting damping, relres = 5.432209e-01 NEWTON: damping accepted, relres = 2.174557e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 2.174557e-01 PMG: contraction number = 2.174557e-01 NEWTON: using errtol_s: 1.699528e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.533700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.007321e+05 PMG: contraction number = , 1.007321e+05 PMG: iteration = 2 PMG: relative residual = 5.284142e-02 PMG: contraction number = 2.429985e-01 NEWTON: using errtol_s: 4.129827e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.471025e+04 PMG: contraction number = , 2.471025e+04 PMG: iteration = 3 PMG: relative residual = 1.709607e-02 PMG: contraction number = 3.235354e-01 NEWTON: using errtol_s: 1.336145e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.629700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.081306e+04 PMG: contraction number = , 1.081306e+04 PMG: iteration = 4 PMG: relative residual = 5.986670e-03 PMG: contraction number = 3.501782e-01 NEWTON: using errtol_s: 4.678890e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.677800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.250059e+03 PMG: contraction number = , 5.250059e+03 PMG: iteration = 5 PMG: relative residual = 2.018992e-03 PMG: contraction number = 3.372480e-01 NEWTON: using errtol_s: 1.577946e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.726000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.254873e+03 PMG: contraction number = , 2.254873e+03 PMG: iteration = 6 PMG: relative residual = 5.815416e-04 PMG: contraction number = 2.880356e-01 NEWTON: using errtol_s: 4.545045e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.774200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.599060e+02 PMG: contraction number = , 7.599060e+02 PMG: iteration = 7 PMG: relative residual = 1.241741e-04 PMG: contraction number = 2.135258e-01 NEWTON: using errtol_s: 9.704845e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.822400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.682666e+02 PMG: contraction number = , 1.682666e+02 PMG: iteration = 8 PMG: relative residual = 1.980324e-05 PMG: contraction number = 1.594796e-01 NEWTON: using errtol_s: 1.547725e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.870500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.503397e+01 PMG: contraction number = , 2.503397e+01 PMG: iteration = 9 PMG: relative residual = 2.880334e-06 PMG: contraction number = 1.454476e-01 NEWTON: using errtol_s: 2.251128e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.918600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.296833e+00 PMG: contraction number = , 4.296833e+00 PMG: iteration = 10 PMG: relative residual = 4.947849e-07 PMG: contraction number = 1.717804e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 5.184000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.476000e+01 Vpmg_setPart: lower corner = (-10.5825, -15.39, -10.7447) Vpmg_setPart: upper corner = (96.9715, 119.284, 98.2627) Vpmg_setPart: actual minima = (-10.5825, -15.39, -10.7447) Vpmg_setPart: actual maxima = (96.9715, 119.284, 98.2627) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 43.4294 Vpbe_ctor2: solute dimensions = 63.267 x 79.22 x 64.122 Vpbe_ctor2: solute charge = -19.9947 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.5 max radius Vclist_setupGrid: Grid lengths = (73.021, 88.774, 73.876) Vclist_setupGrid: Grid lower corner = (6.684, 7.66, 6.821) Vclist_assignAtoms: Have 6790439 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 237.787 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 161, ny = 193, nz = 161 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 21, nyc = 25, nzc = 21 Vpmg_ctor2: PMG chose nf = 5002753, nc = 11025 Vpmg_ctor2: PMG chose narr = 5732564, narrc = 729811 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 71404397, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = 1.561, 2.337, 1.698 VPMG::focusFillBound -- New mesh maxs = 84.828, 101.557, 85.82 VPMG::focusFillBound -- Old mesh mins = -10.5825, -15.39, -10.7447 VPMG::focusFillBound -- Old mesh maxs = 96.9715, 119.284, 98.2627 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoPermanentMultipole... fillcoPermanentMultipole: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.589000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 9.000000e-01 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 1.850000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.140400e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 9.751360e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.178200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.407850e+06 PMG: contraction number = , 1.407850e+06 NEWTON: attempting damping, relres = 2.208698e-01 NEWTON: attempting damping, relres = 5.600034e-01 NEWTON: damping accepted, relres = 2.208698e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 2.208698e-01 PMG: contraction number = 2.208698e-01 NEWTON: using errtol_s: 2.153781e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.689721e+05 PMG: contraction number = , 1.689721e+05 PMG: iteration = 2 PMG: relative residual = 4.666460e-02 PMG: contraction number = 2.112765e-01 NEWTON: using errtol_s: 4.550433e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.294500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.484775e+04 PMG: contraction number = , 3.484775e+04 PMG: iteration = 3 PMG: relative residual = 1.385073e-02 PMG: contraction number = 2.968145e-01 NEWTON: using errtol_s: 1.350635e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.343300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.256569e+04 PMG: contraction number = , 1.256569e+04 PMG: iteration = 4 PMG: relative residual = 4.646743e-03 PMG: contraction number = 3.354872e-01 NEWTON: using errtol_s: 4.531206e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.392200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.498473e+03 PMG: contraction number = , 5.498473e+03 PMG: iteration = 5 PMG: relative residual = 1.520277e-03 PMG: contraction number = 3.271704e-01 NEWTON: using errtol_s: 1.482477e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.440800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.224511e+03 PMG: contraction number = , 2.224511e+03 PMG: iteration = 6 PMG: relative residual = 4.233764e-04 PMG: contraction number = 2.784864e-01 NEWTON: using errtol_s: 4.128495e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.490100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.150105e+02 PMG: contraction number = , 7.150105e+02 PMG: iteration = 7 PMG: relative residual = 8.761384e-05 PMG: contraction number = 2.069408e-01 NEWTON: using errtol_s: 8.543540e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.538800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.487362e+02 PMG: contraction number = , 1.487362e+02 PMG: iteration = 8 PMG: relative residual = 1.385040e-05 PMG: contraction number = 1.580847e-01 NEWTON: using errtol_s: 1.350603e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.588400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.358255e+01 PMG: contraction number = , 2.358255e+01 PMG: iteration = 9 PMG: relative residual = 2.174065e-06 PMG: contraction number = 1.569676e-01 NEWTON: using errtol_s: 2.120009e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.637600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.871009e+00 PMG: contraction number = , 5.871009e+00 PMG: iteration = 10 PMG: relative residual = 5.419156e-07 PMG: contraction number = 2.492638e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 5.299000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.598000e+01 Vpmg_setPart: lower corner = (1.561, 2.337, 1.698) Vpmg_setPart: upper corner = (84.828, 101.557, 85.82) Vpmg_setPart: actual minima = (1.561, 2.337, 1.698) Vpmg_setPart: actual maxima = (84.828, 101.557, 85.82) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.720400e+02