############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 13:31:31 2010 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 13:32:31 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 = 5, dime = (193, 193, 193) 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 = 1.33508, 1.36574, 1.32352 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.889505, 0.907542, 0.882708 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 = 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 = 7.394000e+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 = 2.330000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.863000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 3.829880e-02 PMG: contraction number = 3.829880e-02 PMG: iteration = 2 PMG: relative residual = 4.749620e-03 PMG: contraction number = 1.240148e-01 PMG: iteration = 3 PMG: relative residual = 7.377124e-04 PMG: contraction number = 1.553203e-01 PMG: iteration = 4 PMG: relative residual = 1.312951e-04 PMG: contraction number = 1.779760e-01 PMG: iteration = 5 PMG: relative residual = 2.601072e-05 PMG: contraction number = 1.981088e-01 PMG: iteration = 6 PMG: relative residual = 5.649015e-06 PMG: contraction number = 2.171803e-01 PMG: iteration = 7 PMG: relative residual = 1.337026e-06 PMG: contraction number = 2.366830e-01 PMG: iteration = 8 PMG: relative residual = 3.434915e-07 PMG: contraction number = 2.569071e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.000000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.362000e+01 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 = 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 = -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 = 7.891000e+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 = 2.390000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.112900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.902007e-02 PMG: contraction number = 4.902007e-02 PMG: iteration = 2 PMG: relative residual = 5.996338e-03 PMG: contraction number = 1.223242e-01 PMG: iteration = 3 PMG: relative residual = 8.964374e-04 PMG: contraction number = 1.494975e-01 PMG: iteration = 4 PMG: relative residual = 1.506853e-04 PMG: contraction number = 1.680935e-01 PMG: iteration = 5 PMG: relative residual = 2.741719e-05 PMG: contraction number = 1.819499e-01 PMG: iteration = 6 PMG: relative residual = 5.359200e-06 PMG: contraction number = 1.954686e-01 PMG: iteration = 7 PMG: relative residual = 1.164809e-06 PMG: contraction number = 2.173476e-01 PMG: iteration = 8 PMG: relative residual = 2.930836e-07 PMG: contraction number = 2.516151e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.087000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.449000e+01 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 = 2.685700e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Sep 27 13:36:56 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 13:37:38 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 13:38:17 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 13:40:30 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 13:42:18 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 13:42:26 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/08_cluster_concat/cluster_AL.rep.c3_noH.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: (160.21, 154.233, 209.238) Valist_getStatistics: Min atom coordinate: (83.897, 83.562, 133.818) Valist_getStatistics: Molecule center: (122.054, 118.898, 171.528) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 122.285 118.81 171.528 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 122.285 118.81 171.528 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.701013, 0.653608, 0.697198 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.516527, 0.488642, 0.514283 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.73683, 0.747607, 0.737643 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 122.285 118.81 171.528 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 189.582 181.557 238.459 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = 54.9874 56.0641 104.597 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 171.871 165.72 220.899 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 72.698 71.9008 122.157 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 171.871 165.72 220.899 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 72.698 71.9008 122.157 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 = 46.9695 Vpbe_ctor2: solute dimensions = 79.1732 x 73.8192 x 78.7424 Vpbe_ctor2: solute charge = -18 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 = (89.093, 83.451, 88.2) Vclist_setupGrid: Grid lower corner = (77.507, 77.172, 127.428) Vclist_assignAtoms: Have 5612041 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 254.469 Vacc_storeParms: Using 2584-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 = 9.280000e+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 = 7.600000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 1.960000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.272000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 7.756584e-02 PMG: contraction number = 7.756584e-02 PMG: iteration = 2 PMG: relative residual = 9.723713e-03 PMG: contraction number = 1.253608e-01 PMG: iteration = 3 PMG: relative residual = 1.474356e-03 PMG: contraction number = 1.516248e-01 PMG: iteration = 4 PMG: relative residual = 2.476499e-04 PMG: contraction number = 1.679715e-01 PMG: iteration = 5 PMG: relative residual = 4.525723e-05 PMG: contraction number = 1.827468e-01 PMG: iteration = 6 PMG: relative residual = 9.169181e-06 PMG: contraction number = 2.026015e-01 PMG: iteration = 7 PMG: relative residual = 2.361651e-06 PMG: contraction number = 2.575640e-01 PMG: iteration = 8 PMG: relative residual = 7.406445e-07 PMG: contraction number = 3.136130e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.140000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.491000e+01 Vpmg_setPart: lower corner = (54.9874, 56.0641, 104.597) Vpmg_setPart: upper corner = (189.582, 181.557, 238.459) Vpmg_setPart: actual minima = (54.9874, 56.0641, 104.597) Vpmg_setPart: actual maxima = (189.582, 181.557, 238.459) 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 = 46.9695 Vpbe_ctor2: solute dimensions = 79.1732 x 73.8192 x 78.7424 Vpbe_ctor2: solute charge = -18 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 = (89.093, 83.451, 88.2) Vclist_setupGrid: Grid lower corner = (77.507, 77.172, 127.428) Vclist_assignAtoms: Have 5612041 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 254.469 Vacc_storeParms: Using 2584-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 = 72.698, 71.9008, 122.157 VPMG::focusFillBound -- New mesh maxs = 171.871, 165.72, 220.899 VPMG::focusFillBound -- Old mesh mins = 54.9874, 56.0641, 104.597 VPMG::focusFillBound -- Old mesh maxs = 189.582, 181.557, 238.459 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 = 1.060000e+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 = 7.600000e-01 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.130000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.842000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.204548e-01 PMG: contraction number = 1.204548e-01 PMG: iteration = 2 PMG: relative residual = 1.594467e-02 PMG: contraction number = 1.323706e-01 PMG: iteration = 3 PMG: relative residual = 2.462995e-03 PMG: contraction number = 1.544713e-01 PMG: iteration = 4 PMG: relative residual = 4.240511e-04 PMG: contraction number = 1.721689e-01 PMG: iteration = 5 PMG: relative residual = 8.397655e-05 PMG: contraction number = 1.980340e-01 PMG: iteration = 6 PMG: relative residual = 2.288120e-05 PMG: contraction number = 2.724713e-01 PMG: iteration = 7 PMG: relative residual = 8.745599e-06 PMG: contraction number = 3.822176e-01 PMG: iteration = 8 PMG: relative residual = 3.380822e-06 PMG: contraction number = 3.865741e-01 PMG: iteration = 9 PMG: relative residual = 1.380701e-06 PMG: contraction number = 4.083921e-01 PMG: iteration = 10 PMG: relative residual = 5.535142e-07 PMG: contraction number = 4.008936e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.091000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.429000e+01 Vpmg_setPart: lower corner = (72.698, 71.9008, 122.157) Vpmg_setPart: upper corner = (171.871, 165.72, 220.899) Vpmg_setPart: actual minima = (72.698, 71.9008, 122.157) Vpmg_setPart: actual maxima = (171.871, 165.72, 220.899) 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 = 1.455000e+02