############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:29:35 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:29:46 2011 ############################################################################## 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/116_1XCK_apo/results/traj_heptamer/last_frame_hept_1.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 54845 atoms Valist_getStatistics: Max atom coordinate: (161.187, 195.611, 210.341) Valist_getStatistics: Min atom coordinate: (13.211, 45.307, 66.104) Valist_getStatistics: Molecule center: (87.199, 120.459, 138.222) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.33322, 1.35534, 1.30221 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.888417, 0.901427, 0.870172 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666367, 0.665092, 0.668228 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 215.189 250.687 263.317 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -40.7906 -9.5389 13.2924 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.911 34.037 54.768 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.911 34.037 54.768 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.019700e+02 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 = 1.250000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.690000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068200e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.656185e-02 PMG: contraction number = 4.656185e-02 PMG: iteration = 2 PMG: relative residual = 4.173017e-03 PMG: contraction number = 8.962308e-02 PMG: iteration = 3 PMG: relative residual = 5.508782e-04 PMG: contraction number = 1.320096e-01 PMG: iteration = 4 PMG: relative residual = 9.380117e-05 PMG: contraction number = 1.702757e-01 PMG: iteration = 5 PMG: relative residual = 1.886770e-05 PMG: contraction number = 2.011457e-01 PMG: iteration = 6 PMG: relative residual = 4.311026e-06 PMG: contraction number = 2.284871e-01 PMG: iteration = 7 PMG: relative residual = 1.077707e-06 PMG: contraction number = 2.499885e-01 PMG: iteration = 8 PMG: relative residual = 2.899351e-07 PMG: contraction number = 2.690296e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.764000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.196000e+01 Vpmg_setPart: lower corner = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: upper corner = (215.189, 250.687, 263.317) Vpmg_setPart: actual minima = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: actual maxima = (215.189, 250.687, 263.317) 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.911, 34.037, 54.768 VPMG::focusFillBound -- New mesh maxs = 172.487, 207.111, 221.841 VPMG::focusFillBound -- Old mesh mins = -40.7906, -9.5389, 13.2924 VPMG::focusFillBound -- Old mesh maxs = 215.189, 250.687, 263.317 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 = 1.068600e+02 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 = 1.250000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.700000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.357200e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 6.535572e-02 PMG: contraction number = 6.535572e-02 PMG: iteration = 2 PMG: relative residual = 5.807681e-03 PMG: contraction number = 8.886262e-02 PMG: iteration = 3 PMG: relative residual = 6.989536e-04 PMG: contraction number = 1.203499e-01 PMG: iteration = 4 PMG: relative residual = 1.026494e-04 PMG: contraction number = 1.468616e-01 PMG: iteration = 5 PMG: relative residual = 1.694391e-05 PMG: contraction number = 1.650658e-01 PMG: iteration = 6 PMG: relative residual = 3.278296e-06 PMG: contraction number = 1.934793e-01 PMG: iteration = 7 PMG: relative residual = 8.286698e-07 PMG: contraction number = 2.527746e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.545000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.972000e+01 Vpmg_setPart: lower corner = (1.911, 34.037, 54.768) Vpmg_setPart: upper corner = (172.487, 207.111, 221.841) Vpmg_setPart: actual minima = (1.911, 34.037, 54.768) Vpmg_setPart: actual maxima = (172.487, 207.111, 221.841) 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 = 2.579500e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:29:48 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:29:56 2011 ############################################################################## 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/116_1XCK_apo/results/traj_heptamer/last_frame_hept_1.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 54845 atoms Valist_getStatistics: Max atom coordinate: (161.187, 195.611, 210.341) Valist_getStatistics: Min atom coordinate: (13.211, 45.307, 66.104) Valist_getStatistics: Molecule center: (87.199, 120.459, 138.222) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.33322, 1.35534, 1.30221 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.888417, 0.901427, 0.870172 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666367, 0.665092, 0.668228 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 215.189 250.687 263.317 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -40.7906 -9.5389 13.2924 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.911 34.037 54.768 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.911 34.037 54.768 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.020600e+02 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 = 1.250000e+00 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 = 1.069300e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.656185e-02 PMG: contraction number = 4.656185e-02 PMG: iteration = 2 PMG: relative residual = 4.173017e-03 PMG: contraction number = 8.962308e-02 PMG: iteration = 3 PMG: relative residual = 5.508782e-04 PMG: contraction number = 1.320096e-01 PMG: iteration = 4 PMG: relative residual = 9.380117e-05 PMG: contraction number = 1.702757e-01 PMG: iteration = 5 PMG: relative residual = 1.886770e-05 PMG: contraction number = 2.011457e-01 PMG: iteration = 6 PMG: relative residual = 4.311026e-06 PMG: contraction number = 2.284871e-01 PMG: iteration = 7 PMG: relative residual = 1.077707e-06 PMG: contraction number = 2.499885e-01 PMG: iteration = 8 PMG: relative residual = 2.899351e-07 PMG: contraction number = 2.690296e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.765000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.199000e+01 Vpmg_setPart: lower corner = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: upper corner = (215.189, 250.687, 263.317) Vpmg_setPart: actual minima = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: actual maxima = (215.189, 250.687, 263.317) 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.911, 34.037, 54.768 VPMG::focusFillBound -- New mesh maxs = 172.487, 207.111, 221.841 VPMG::focusFillBound -- Old mesh mins = -40.7906, -9.5389, 13.2924 VPMG::focusFillBound -- Old mesh maxs = 215.189, 250.687, 263.317 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: Fri Jan 14 16:42:12 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:42:21 2011 ############################################################################## 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/116_1XCK_apo/results/traj_heptamer/last_frame_hept_1.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 54845 atoms Valist_getStatistics: Max atom coordinate: (161.187, 195.611, 210.341) Valist_getStatistics: Min atom coordinate: (13.211, 45.307, 66.104) Valist_getStatistics: Molecule center: (87.199, 120.459, 138.222) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 1.33322, 1.35534, 1.30221 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.888417, 0.901427, 0.870172 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666367, 0.665092, 0.668228 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 87.199 120.574 138.304 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 215.189 250.687 263.317 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -40.7906 -9.5389 13.2924 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = 1.911 34.037 54.768 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 172.487 207.111 221.841 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = 1.911 34.037 54.768 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.020000e+02 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 = 1.250000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.690000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 4.656185e-02 PMG: contraction number = 4.656185e-02 PMG: iteration = 2 PMG: relative residual = 4.173017e-03 PMG: contraction number = 8.962308e-02 PMG: iteration = 3 PMG: relative residual = 5.508782e-04 PMG: contraction number = 1.320096e-01 PMG: iteration = 4 PMG: relative residual = 9.380117e-05 PMG: contraction number = 1.702757e-01 PMG: iteration = 5 PMG: relative residual = 1.886770e-05 PMG: contraction number = 2.011457e-01 PMG: iteration = 6 PMG: relative residual = 4.311026e-06 PMG: contraction number = 2.284871e-01 PMG: iteration = 7 PMG: relative residual = 1.077707e-06 PMG: contraction number = 2.499885e-01 PMG: iteration = 8 PMG: relative residual = 2.899351e-07 PMG: contraction number = 2.690296e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.762000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.189000e+01 Vpmg_setPart: lower corner = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: upper corner = (215.189, 250.687, 263.317) Vpmg_setPart: actual minima = (-40.7906, -9.5389, 13.2924) Vpmg_setPart: actual maxima = (215.189, 250.687, 263.317) 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 = 82.6415 Vpbe_ctor2: solute dimensions = 150.576 x 153.074 x 147.073 Vpbe_ctor2: solute charge = -125.963 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 = (160.188, 162.516, 156.449) Vclist_setupGrid: Grid lower corner = (7.105, 39.201, 59.998) Vclist_assignAtoms: Have 10019596 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 = 1.911, 34.037, 54.768 VPMG::focusFillBound -- New mesh maxs = 172.487, 207.111, 221.841 VPMG::focusFillBound -- Old mesh mins = -40.7906, -9.5389, 13.2924 VPMG::focusFillBound -- Old mesh maxs = 215.189, 250.687, 263.317 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 = 1.068800e+02 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 = 1.250000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 2.700000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.356900e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 6.535572e-02 PMG: contraction number = 6.535572e-02 PMG: iteration = 2 PMG: relative residual = 5.807681e-03 PMG: contraction number = 8.886262e-02 PMG: iteration = 3 PMG: relative residual = 6.989536e-04 PMG: contraction number = 1.203499e-01 PMG: iteration = 4 PMG: relative residual = 1.026494e-04 PMG: contraction number = 1.468616e-01 PMG: iteration = 5 PMG: relative residual = 1.694391e-05 PMG: contraction number = 1.650658e-01 PMG: iteration = 6 PMG: relative residual = 3.278296e-06 PMG: contraction number = 1.934793e-01 PMG: iteration = 7 PMG: relative residual = 8.286698e-07 PMG: contraction number = 2.527746e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.543000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.970000e+01 Vpmg_setPart: lower corner = (1.911, 34.037, 54.768) Vpmg_setPart: upper corner = (172.487, 207.111, 221.841) Vpmg_setPart: actual minima = (1.911, 34.037, 54.768) Vpmg_setPart: actual maxima = (172.487, 207.111, 221.841) 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 = 2.580600e+02 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Sun Jan 16 21:34:59 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Sun Jan 16 21:35:11 2011 ############################################################################## 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 last_frame.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=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 mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) 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 mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (77.626, 123.586, 100.757) Valist_getStatistics: Min atom coordinate: (-68.445, 42.443, -43.746) Valist_getStatistics: Molecule center: (4.5905, 83.0145, 28.5055) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.720178, 0.741033, 0.785323 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.480452, 0.540069, 0.524454 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.66713, 0.728805, 0.66782 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 131.342 154.154 154.157 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -122.161 11.8753 -97.1461 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 89.1501 134.861 112.418 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -79.9691 31.1679 -55.4072 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 89.1501 134.861 112.418 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -79.9691 31.1679 -55.4072 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.720178, 0.741033, 0.785323 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.480452, 0.540069, 0.524454 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.66713, 0.728805, 0.66782 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 4.5905 83.0145 28.5055 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 131.342 154.154 154.157 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -122.161 11.8753 -97.1461 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 89.1501 134.861 112.418 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -79.9691 31.1679 -55.4072 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 89.1501 134.861 112.418 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -79.9691 31.1679 -55.4072 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.5322 Vpbe_ctor2: solute dimensions = 149.119 x 83.6932 x 147.825 Vpbe_ctor2: solute charge = -126 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 7042.98 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 1.9 max radius Vclist_setupGrid: Grid lengths = (157.147, 92.219, 155.579) Vclist_setupGrid: Grid lower corner = (-73.983, 36.905, -49.284) Vclist_assignAtoms: Have 11628103 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 191.134 Vacc_storeParms: Using 1936-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 = 353, ny = 193, nz = 321 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 41 Vpmg_ctor2: PMG chose nf = 21869409, nc = 46125 Vpmg_ctor2: PMG chose narr = 25032984, narrc = 3163575 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 307133093, 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 = 3.920000e+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 = 3.710000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.931000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350600e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.938521e-02 PMG: contraction number = 9.938521e-02 PMG: iteration = 2 PMG: relative residual = 1.102173e-02 PMG: contraction number = 1.108991e-01 PMG: iteration = 3 PMG: relative residual = 1.287164e-03 PMG: contraction number = 1.167842e-01 PMG: iteration = 4 PMG: relative residual = 1.527338e-04 PMG: contraction number = 1.186592e-01 PMG: iteration = 5 PMG: relative residual = 1.858609e-05 PMG: contraction number = 1.216894e-01 PMG: iteration = 6 PMG: relative residual = 2.587217e-06 PMG: contraction number = 1.392018e-01 PMG: iteration = 7 PMG: relative residual = 4.082409e-07 PMG: contraction number = 1.577915e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.116600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.068500e+02 Vpmg_setPart: lower corner = (-122.161, 11.8753, -97.1461) Vpmg_setPart: upper corner = (131.342, 154.154, 154.157) Vpmg_setPart: actual minima = (-122.161, 11.8753, -97.1461) Vpmg_setPart: actual maxima = (131.342, 154.154, 154.157) 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).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.161259053714E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.300000e-01 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 = 81.5322 Vpbe_ctor2: solute dimensions = 149.119 x 83.6932 x 147.825 Vpbe_ctor2: solute charge = -126 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 7042.98 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 1.9 max radius Vclist_setupGrid: Grid lengths = (157.147, 92.219, 155.579) Vclist_setupGrid: Grid lower corner = (-73.983, 36.905, -49.284) Vclist_assignAtoms: Have 11628103 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 191.134 Vacc_storeParms: Using 1936-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 = 353, ny = 193, nz = 321 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 41 Vpmg_ctor2: PMG chose nf = 21869409, nc = 46125 Vpmg_ctor2: PMG chose narr = 25032984, narrc = 3163575 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 307133093, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -79.9691, 31.1679, -55.4072 VPMG::focusFillBound -- New mesh maxs = 89.1501, 134.861, 112.418 VPMG::focusFillBound -- Old mesh mins = -122.161, 11.8753, -97.1461 VPMG::focusFillBound -- Old mesh maxs = 131.342, 154.154, 154.157 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: upper corner = (89.1501, 134.861, 112.418) Vpmg_setPart: actual minima = (-122.161, 11.8753, -97.1461) Vpmg_setPart: actual maxima = (131.342, 154.154, 154.157) 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 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-79.9691, 31.1679, -55.4072) VPMG::extEnergy Disj part upper corner = (89.1501, 134.861, 112.418) VPMG::extEnergy Old lower corner = (-122.161, 11.8753, -97.1461) VPMG::extEnergy Old upper corner = (131.342, 154.154, 154.157) Vpmg_qmEnergy: Zero energy for zero ionic strength! VPMG::extEnergy: extQmEnergy = 0 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 187.02 kT 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 = 5.488000e+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 = 3.330000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.246000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.924500e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.173504e-01 PMG: contraction number = 1.173504e-01 PMG: iteration = 2 PMG: relative residual = 1.424668e-02 PMG: contraction number = 1.214029e-01 PMG: iteration = 3 PMG: relative residual = 1.854539e-03 PMG: contraction number = 1.301734e-01 PMG: iteration = 4 PMG: relative residual = 2.549463e-04 PMG: contraction number = 1.374715e-01 PMG: iteration = 5 PMG: relative residual = 3.663694e-05 PMG: contraction number = 1.437045e-01 PMG: iteration = 6 PMG: relative residual = 5.515191e-06 PMG: contraction number = 1.505364e-01 PMG: iteration = 7 PMG: relative residual = 8.390495e-07 PMG: contraction number = 1.521343e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.120300e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.006200e+02 Vpmg_setPart: lower corner = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: upper corner = (89.1501, 134.861, 112.418) Vpmg_setPart: actual minima = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: actual maxima = (89.1501, 134.861, 112.418) 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).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.498924722652E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.600000e-01 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_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.5322 Vpbe_ctor2: solute dimensions = 149.119 x 83.6932 x 147.825 Vpbe_ctor2: solute charge = -126 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 7042.98 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 1.9 max radius Vclist_setupGrid: Grid lengths = (157.147, 92.219, 155.579) Vclist_setupGrid: Grid lower corner = (-73.983, 36.905, -49.284) Vclist_assignAtoms: Have 11628103 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 191.134 Vacc_storeParms: Using 1936-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 = 353, ny = 193, nz = 321 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 41 Vpmg_ctor2: PMG chose nf = 21869409, nc = 46125 Vpmg_ctor2: PMG chose narr = 25032984, narrc = 3163575 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 307133093, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.710000e+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 = 3.340000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 9.481000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.350400e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.245009e-02 PMG: contraction number = 9.245009e-02 PMG: iteration = 2 PMG: relative residual = 9.625031e-03 PMG: contraction number = 1.041106e-01 PMG: iteration = 3 PMG: relative residual = 1.046164e-03 PMG: contraction number = 1.086921e-01 PMG: iteration = 4 PMG: relative residual = 1.165420e-04 PMG: contraction number = 1.113993e-01 PMG: iteration = 5 PMG: relative residual = 1.319164e-05 PMG: contraction number = 1.131921e-01 PMG: iteration = 6 PMG: relative residual = 1.510403e-06 PMG: contraction number = 1.144970e-01 PMG: iteration = 7 PMG: relative residual = 1.748187e-07 PMG: contraction number = 1.157431e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 1.136100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.144800e+02 Vpmg_setPart: lower corner = (-122.161, 11.8753, -97.1461) Vpmg_setPart: upper corner = (131.342, 154.154, 154.157) Vpmg_setPart: actual minima = (-122.161, 11.8753, -97.1461) Vpmg_setPart: actual maxima = (131.342, 154.154, 154.157) 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).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.300074241591E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.400000e-01 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 = 81.5322 Vpbe_ctor2: solute dimensions = 149.119 x 83.6932 x 147.825 Vpbe_ctor2: solute charge = -126 Vpbe_ctor2: bulk ionic strength = 0 Vpbe_ctor2: xkappa = 0 Vpbe_ctor2: Debye length = 0 Vpbe_ctor2: zkappa2 = 0 Vpbe_ctor2: zmagic = 7042.98 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 1.9 max radius Vclist_setupGrid: Grid lengths = (157.147, 92.219, 155.579) Vclist_setupGrid: Grid lower corner = (-73.983, 36.905, -49.284) Vclist_assignAtoms: Have 11628103 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 191.134 Vacc_storeParms: Using 1936-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 = 353, ny = 193, nz = 321 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 41 Vpmg_ctor2: PMG chose nf = 21869409, nc = 46125 Vpmg_ctor2: PMG chose narr = 25032984, narrc = 3163575 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 307133093, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -79.9691, 31.1679, -55.4072 VPMG::focusFillBound -- New mesh maxs = 89.1501, 134.861, 112.418 VPMG::focusFillBound -- Old mesh mins = -122.161, 11.8753, -97.1461 VPMG::focusFillBound -- Old mesh maxs = 131.342, 154.154, 154.157 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: upper corner = (89.1501, 134.861, 112.418) Vpmg_setPart: actual minima = (-122.161, 11.8753, -97.1461) Vpmg_setPart: actual maxima = (131.342, 154.154, 154.157) 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 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-79.9691, 31.1679, -55.4072) VPMG::extEnergy Disj part upper corner = (89.1501, 134.861, 112.418) VPMG::extEnergy Old lower corner = (-122.161, 11.8753, -97.1461) VPMG::extEnergy Old upper corner = (131.342, 154.154, 154.157) Vpmg_qmEnergy: Zero energy for zero ionic strength! VPMG::extEnergy: extQmEnergy = 0 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 7165 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.052000e+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 = 2.960000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.199000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.490400e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.047261e-01 PMG: contraction number = 1.047261e-01 PMG: iteration = 2 PMG: relative residual = 1.131384e-02 PMG: contraction number = 1.080326e-01 PMG: iteration = 3 PMG: relative residual = 1.294944e-03 PMG: contraction number = 1.144567e-01 PMG: iteration = 4 PMG: relative residual = 1.519199e-04 PMG: contraction number = 1.173177e-01 PMG: iteration = 5 PMG: relative residual = 1.810657e-05 PMG: contraction number = 1.191850e-01 PMG: iteration = 6 PMG: relative residual = 2.183712e-06 PMG: contraction number = 1.206033e-01 PMG: iteration = 7 PMG: relative residual = 2.658406e-07 PMG: contraction number = 1.217379e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 9.846000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.855000e+02 Vpmg_setPart: lower corner = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: upper corner = (89.1501, 134.861, 112.418) Vpmg_setPart: actual minima = (-79.9691, 31.1679, -55.4072) Vpmg_setPart: actual maxima = (89.1501, 134.861, 112.418) 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).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.636103462197E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.500000e-01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 9.504700e+02