############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 21:36:20 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 Dec 1 21:39:06 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/24_browdye/cis.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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (77.814, 120.756, 83.994) Valist_getStatistics: Min atom coordinate: (-69.221, 42.789, -60.367) Valist_getStatistics: Molecule center: (4.2965, 81.7725, 11.8135) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.722669, 0.715124, 0.781793 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.481918, 0.524828, 0.522378 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666858, 0.733898, 0.66818 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 131.486 150.324 137 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -122.893 13.0206 -113.173 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -80.521 31.289 -71.667 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -80.521 31.289 -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 = 79.3531 Vpbe_ctor2: solute dimensions = 149.635 x 80.767 x 147.161 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 = (159.247, 90.179, 156.573) Vclist_setupGrid: Grid lower corner = (-75.327, 36.683, -66.473) Vclist_assignAtoms: Have 15003051 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 = 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... ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 21:40:20 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 Dec 1 21:40:35 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/24_browdye/trans.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... ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 22:13:17 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/24_browdye/cis.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 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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 22:13:54 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/24_browdye/cis.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 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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 22:14:47 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 /net/lutefisk/slars/groel_md/1XCK/analysis/24_browdye/cis.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 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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (77.814, 120.756, 83.994) Valist_getStatistics: Min atom coordinate: (-69.221, 42.789, -60.367) Valist_getStatistics: Molecule center: (4.2965, 81.7725, 11.8135) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.722669, 0.715124, 0.781793 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.481918, 0.524828, 0.522378 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666858, 0.733898, 0.66818 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 131.486 150.324 137 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -122.893 13.0206 -113.173 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -80.521 31.289 -71.667 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -80.521 31.289 -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 = 79.3531 Vpbe_ctor2: solute dimensions = 149.635 x 80.767 x 147.161 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 = (159.247, 90.179, 156.573) Vclist_setupGrid: Grid lower corner = (-75.327, 36.683, -66.473) Vclist_assignAtoms: Have 15003051 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 = 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... ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 22:15:43 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 /net/lutefisk/slars/groel_md/1XCK/analysis/24_browdye/cis.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 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 = (353, 193, 321) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (77.814, 120.756, 83.994) Valist_getStatistics: Min atom coordinate: (-69.221, 42.789, -60.367) Valist_getStatistics: Molecule center: (4.2965, 81.7725, 11.8135) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.722669, 0.715124, 0.781793 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.481918, 0.524828, 0.522378 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666858, 0.733898, 0.66818 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 4.2965 81.6725 11.9135 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 131.486 150.324 137 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -122.893 13.0206 -113.173 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -80.521 31.289 -71.667 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 89.114 132.056 95.494 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -80.521 31.289 -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 = 79.3531 Vpbe_ctor2: solute dimensions = 149.635 x 80.767 x 147.161 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 = (159.247, 90.179, 156.573) Vclist_setupGrid: Grid lower corner = (-75.327, 36.683, -66.473) Vclist_assignAtoms: Have 15003051 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 = 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... ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Wed Dec 1 22:15:52 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 /net/lutefisk/slars/groel_md/1XCK/analysis/24_browdye/trans.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 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 = (353, 193, 353) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (76.218, 47.211, 86.513) Valist_getStatistics: Min atom coordinate: (-70.371, -30.892, -59.612) Valist_getStatistics: Molecule center: (2.9235, 8.1595, 13.4505) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 2.9755 8.2595 13.4505 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.9755 8.2595 13.4505 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.721017, 0.716329, 0.718274 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.480946, 0.525536, 0.479332 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.667038, 0.733653, 0.667339 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 2.9755 8.2595 13.4505 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 129.875 77.0271 139.867 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -123.924 -60.508 -112.966 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 87.622 58.711 97.813 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -81.671 -42.192 -70.912 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 87.622 58.711 97.813 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -81.671 -42.192 -70.912 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 = 79.6455 Vpbe_ctor2: solute dimensions = 149.293 x 80.903 x 148.725 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 = (158.801, 90.315, 158.337) Vclist_setupGrid: Grid lower corner = (-76.477, -36.998, -65.718) Vclist_assignAtoms: Have 14896256 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 = 353, ny = 193, nz = 353 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 45 Vpmg_ctor2: PMG chose nf = 24049537, nc = 50625 Vpmg_ctor2: PMG chose narr = 27527204, narrc = 3477667 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 337810321, 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 = 5.108000e+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 = 2.290000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. 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 = 5.315000e+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 = 2.540000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 4.085000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.652000e+01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 8.101720e-02 PMG: contraction number = 8.101720e-02 PMG: iteration = 2 PMG: relative residual = 1.309308e-02 PMG: contraction number = 1.616086e-01 PMG: iteration = 3 PMG: relative residual = 4.119505e-03 PMG: contraction number = 3.146323e-01 PMG: iteration = 4 PMG: relative residual = 1.200426e-03 PMG: contraction number = 2.914004e-01 PMG: iteration = 5 PMG: relative residual = 6.885401e-04 PMG: contraction number = 5.735799e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 5.120000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.164800e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 6 PMG: relative residual = 2.364591e-04 PMG: contraction number = 3.434210e-01 PMG: iteration = 1 PMG: relative residual = 8.459857e-02 PMG: contraction number = 8.459857e-02 PMG: iteration = 7 PMG: relative residual = 1.563993e-04 PMG: contraction number = 6.614220e-01 PMG: iteration = 2 PMG: relative residual = 1.405418e-02 PMG: contraction number = 1.661279e-01 PMG: iteration = 8 PMG: relative residual = 5.476824e-05 PMG: contraction number = 3.501822e-01 PMG: iteration = 9 PMG: relative residual = 3.737208e-05 PMG: contraction number = 6.823677e-01 PMG: iteration = 3 PMG: relative residual = 4.722260e-03 PMG: contraction number = 3.360038e-01 PMG: iteration = 4 PMG: relative residual = 1.446772e-03 PMG: iteration = 10 PMG: contraction number = 3.063727e-01 PMG: relative residual = 1.312334e-05 PMG: contraction number = 3.511535e-01 PMG: iteration = 11 PMG: relative residual = 9.067043e-06 PMG: contraction number = 6.909099e-01 PMG: iteration = 5 PMG: relative residual = 8.722280e-04 PMG: contraction number = 6.028789e-01 PMG: iteration = 12 PMG: relative residual = 3.191963e-06 PMG: contraction number = 3.520401e-01 PMG: iteration = 6 PMG: relative residual = 3.095986e-04 PMG: contraction number = 3.549514e-01 PMG: iteration = 13 PMG: relative residual = 2.219200e-06 PMG: contraction number = 6.952463e-01 PMG: iteration = 7 PMG: relative residual = 2.120694e-04 PMG: contraction number = 6.849818e-01 PMG: iteration = 14 PMG: relative residual = 7.845204e-07 PMG: contraction number = 3.535149e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.460000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.908400e+02 Vpmg_setPart: lower corner = (-122.893, 13.0206, -113.173) Vpmg_setPart: upper corner = (131.486, 150.324, 137) Vpmg_setPart: actual minima = (-122.893, 13.0206, -113.173) Vpmg_setPart: actual maxima = (131.486, 150.324, 137) 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 = 79.3531 Vpbe_ctor2: solute dimensions = 149.635 x 80.767 x 147.161 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 = (159.247, 90.179, 156.573) Vclist_setupGrid: Grid lower corner = (-75.327, 36.683, -66.473) Vclist_assignAtoms: Have 15003051 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 = 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 = -80.521, 31.289, -71.667 VPMG::focusFillBound -- New mesh maxs = 89.114, 132.056, 95.494 VPMG::focusFillBound -- Old mesh mins = -122.893, 13.0206, -113.173 VPMG::focusFillBound -- Old mesh maxs = 131.486, 150.324, 137 PMG: iteration = 8 PMG: relative residual = 7.672546e-05 PMG: contraction number = 3.617941e-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 = 9 PMG: relative residual = 5.413426e-05 PMG: contraction number = 7.055580e-01 PMG: iteration = 10 PMG: relative residual = 1.968550e-05 PMG: contraction number = 3.636422e-01 PMG: iteration = 11 PMG: relative residual = 1.404524e-05 PMG: contraction number = 7.134815e-01 PMG: iteration = 12 PMG: relative residual = 5.129647e-06 PMG: contraction number = 3.652231e-01 PMG: iteration = 13 PMG: relative residual = 3.678439e-06 PMG: contraction number = 7.170940e-01 PMG: iteration = 14 PMG: relative residual = 1.350919e-06 PMG: contraction number = 3.672532e-01 PMG: iteration = 15 PMG: relative residual = 9.704221e-07 PMG: contraction number = 7.183423e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 5.883400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.511000e+02 Vpmg_setPart: lower corner = (-123.924, -60.508, -112.966) Vpmg_setPart: upper corner = (129.875, 77.0271, 139.867) Vpmg_setPart: actual minima = (-123.924, -60.508, -112.966) Vpmg_setPart: actual maxima = (129.875, 77.0271, 139.867) 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 = 79.6455 Vpbe_ctor2: solute dimensions = 149.293 x 80.903 x 148.725 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 = (158.801, 90.315, 158.337) Vclist_setupGrid: Grid lower corner = (-76.477, -36.998, -65.718) Vclist_assignAtoms: Have 14896256 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 = 353, ny = 193, nz = 353 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 45, nyc = 25, nzc = 45 Vpmg_ctor2: PMG chose nf = 24049537, nc = 50625 Vpmg_ctor2: PMG chose narr = 27527204, narrc = 3477667 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 337810321, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -81.671, -42.192, -70.912 VPMG::focusFillBound -- New mesh maxs = 87.622, 58.711, 97.813 VPMG::focusFillBound -- Old mesh mins = -123.924, -60.508, -112.966 VPMG::focusFillBound -- Old mesh maxs = 129.875, 77.0271, 139.867 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 = 6.804000e+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 = 2.100000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.910000e+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 = 2.300000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 4.126000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.636800e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.339227e-01 PMG: contraction number = 1.339227e-01 PMG: iteration = 2 PMG: relative residual = 1.967894e-02 PMG: contraction number = 1.469426e-01 PMG: iteration = 3 PMG: relative residual = 4.521373e-03 PMG: contraction number = 2.297569e-01 PMG: iteration = 4 PMG: relative residual = 1.241862e-03 PMG: contraction number = 2.746648e-01 PMG: iteration = 5 PMG: relative residual = 6.411138e-04 PMG: contraction number = 5.162520e-01 PMG: iteration = 6 PMG: relative residual = 2.451796e-04 PMG: contraction number = 3.824276e-01 PMG: iteration = 7 PMG: relative residual = 1.668738e-04 PMG: contraction number = 6.806185e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 6.370000e+01 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. PMG: iteration = 8 PMG: relative residual = 6.710366e-05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.490100e+02 PMG: contraction number = 4.021223e-01 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 1.396715e-01 PMG: contraction number = 1.396715e-01 PMG: iteration = 9 PMG: relative residual = 4.988199e-05 PMG: contraction number = 7.433572e-01 PMG: iteration = 2 PMG: relative residual = 2.080281e-02 PMG: contraction number = 1.489410e-01 PMG: iteration = 10 PMG: relative residual = 2.043413e-05 PMG: contraction number = 4.096494e-01 PMG: iteration = 3 PMG: relative residual = 4.958772e-03 PMG: contraction number = 2.383703e-01 PMG: iteration = 11 PMG: relative residual = 1.563795e-05 PMG: contraction number = 7.652858e-01 PMG: iteration = 4 PMG: relative residual = 1.390077e-03 PMG: contraction number = 2.803268e-01 PMG: iteration = 12 PMG: relative residual = 6.563043e-06 PMG: contraction number = 4.196869e-01 PMG: iteration = 5 PMG: relative residual = 7.639527e-04 PMG: contraction number = 5.495758e-01 PMG: iteration = 13 PMG: relative residual = 4.997463e-06 PMG: contraction number = 7.614552e-01 PMG: iteration = 6 PMG: relative residual = 2.941040e-04 PMG: contraction number = 3.849767e-01 PMG: iteration = 14 PMG: relative residual = 2.182473e-06 PMG: contraction number = 4.367161e-01 PMG: iteration = 7 PMG: relative residual = 2.108801e-04 PMG: contraction number = 7.170254e-01 PMG: iteration = 15 PMG: relative residual = 1.618132e-06 PMG: iteration = 8 PMG: relative residual = 8.460747e-05 PMG: contraction number = 7.414213e-01 PMG: contraction number = 4.012113e-01 PMG: iteration = 16 PMG: relative residual = 7.452531e-07 PMG: contraction number = 4.605639e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.360800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.882300e+02 Vpmg_setPart: lower corner = (-80.521, 31.289, -71.667) Vpmg_setPart: upper corner = (89.114, 132.056, 95.494) Vpmg_setPart: actual minima = (-80.521, 31.289, -71.667) Vpmg_setPart: actual maxima = (89.114, 132.056, 95.494) 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 = 9 PMG: relative residual = 6.583312e-05 PMG: contraction number = 7.781005e-01 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 = 10 PMG: relative residual = 2.658230e-05 PMG: contraction number = 4.037830e-01 PMG: iteration = 11 PMG: relative residual = 2.145203e-05 PMG: contraction number = 8.070044e-01 PMG: iteration = 12 PMG: relative residual = 8.673697e-06 PMG: contraction number = 4.043299e-01 PMG: iteration = 13 PMG: relative residual = 7.107927e-06 PMG: contraction number = 8.194806e-01 Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.421280e+03 PMG: iteration = 14 PMG: relative residual = 2.883329e-06 PMG: contraction number = 4.056498e-01 PMG: iteration = 15 PMG: relative residual = 2.373799e-06 PMG: contraction number = 8.232840e-01 PMG: iteration = 16 PMG: relative residual = 9.687613e-07 PMG: contraction number = 4.081059e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 6.516000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.259000e+02 Vpmg_setPart: lower corner = (-81.671, -42.192, -70.912) Vpmg_setPart: upper corner = (87.622, 58.711, 97.813) Vpmg_setPart: actual minima = (-81.671, -42.192, -70.912) Vpmg_setPart: actual maxima = (87.622, 58.711, 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 = 1.521600e+03