############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 18 14:04:08 2014 ############################################################################## 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 piplc_hsp82_bound_to_pcpg_50_50_allh39.926.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb39.926.pdb NOsh: Storing molecule 2 path dmpc_dmpg_50_50.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34067 atoms Valist_getStatistics: Max atom coordinate: (58.908, 62.401, 86.213) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 29.266) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 86.213) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 30.159) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 58.186) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 18 14:04:49 2014 ############################################################################## 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 piplc_hsp82_bound_to_pcpg_50_50_allh39.926.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb39.926.pdb NOsh: Storing molecule 2 path dmpc_dmpg_50_50.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation 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 cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... 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 gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (481, 513, 481) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34067 atoms Valist_getStatistics: Max atom coordinate: (58.908, 62.401, 86.213) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 29.266) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 86.213) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 30.159) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 58.186) Valist_readPDB: Counted 29312 atoms Valist_getStatistics: Max atom coordinate: (58.908, 62.401, 27.159) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, -0.261) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593198 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.341446 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575602 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.633 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.102 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593198 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.341446 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575602 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.633 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.102 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593198 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.341446 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575602 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 2.212 -2.857 29.266 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.633 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.102 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 83.908 87.4015 111.213 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -79.484 -93.1155 -52.681 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 88.8405 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 116.641 Vpbe_ctor2: solute charge = -134.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (127.72, 144.845, 128.222) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 10802895 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.015000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.430000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.917000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220800e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.100298e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.930400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.442431e+06 PMG: contraction number = , 4.442431e+06 NEWTON: attempting damping, relres = 1.248938e+03 NEWTON: attempting damping, relres = 5.642431e-01 NEWTON: attempting damping, relres = 7.733049e-01 NEWTON: damping accepted, relres = 5.642431e-01 PMG: iteration = 1 PMG: relative residual = 5.642431e-01 PMG: contraction number = 5.642431e-01 NEWTON: using errtol_s: 2.313565e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.749800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.493307e+06 PMG: contraction number = , 2.493307e+06 NEWTON: attempting damping, relres = 6.017077e-02 NEWTON: attempting damping, relres = 3.094792e-01 NEWTON: damping accepted, relres = 6.017077e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 6.017077e-02 PMG: contraction number = 1.066398e-01 NEWTON: using errtol_s: 2.467181e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.919000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.495643e+05 PMG: contraction number = , 3.495643e+05 PMG: iteration = 3 PMG: relative residual = 8.925147e-03 PMG: contraction number = 1.483303e-01 NEWTON: using errtol_s: 3.659576e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.768700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.207804e+04 PMG: contraction number = , 6.207804e+04 PMG: iteration = 4 PMG: relative residual = 1.711264e-03 PMG: contraction number = 1.917351e-01 NEWTON: using errtol_s: 7.016691e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.616800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.366393e+04 PMG: contraction number = , 1.366393e+04 PMG: iteration = 5 PMG: relative residual = 3.881641e-04 PMG: contraction number = 2.268289e-01 NEWTON: using errtol_s: 1.591589e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.469000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.810226e+03 PMG: contraction number = , 3.810226e+03 PMG: iteration = 6 PMG: relative residual = 9.965058e-05 PMG: contraction number = 2.567228e-01 NEWTON: using errtol_s: 4.085971e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.354600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.253643e+03 PMG: contraction number = , 1.253643e+03 PMG: iteration = 7 PMG: relative residual = 2.908874e-05 PMG: contraction number = 2.919074e-01 NEWTON: using errtol_s: 1.192725e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.202400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.280334e+02 PMG: contraction number = , 4.280334e+02 PMG: iteration = 8 PMG: relative residual = 9.492033e-06 PMG: contraction number = 3.263130e-01 NEWTON: using errtol_s: 3.892016e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.455259e+02 PMG: contraction number = , 1.455259e+02 PMG: iteration = 9 PMG: relative residual = 3.201778e-06 PMG: contraction number = 3.373122e-01 NEWTON: using errtol_s: 1.312825e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.062449e+01 PMG: contraction number = , 5.062449e+01 PMG: iteration = 10 PMG: relative residual = 1.111883e-06 PMG: contraction number = 3.472703e-01 NEWTON: using errtol_s: 4.559050e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.781531e+01 PMG: contraction number = , 1.781531e+01 PMG: iteration = 11 PMG: relative residual = 3.911035e-07 PMG: contraction number = 3.517489e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.106610e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.147330e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.102) Vpmg_setPart: upper corner = (143.952, 160.29, 171.633) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 8.076678527519E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.202217839247E+05 kT Vpmg_energy: dielEnergy = 4.599605942571E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.845000e+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 = 88.8405 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 116.641 Vpbe_ctor2: solute charge = -134.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (127.72, 144.845, 128.222) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 10802895 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -79.484, -93.1155, -52.681 VPMG::focusFillBound -- New mesh maxs = 83.908, 87.4015, 111.213 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.102 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.633 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 = (-79.484, -93.1155, -52.681) VPMG::extEnergy Disj part upper corner = (83.908, 87.4015, 111.213) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.102) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.633) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0201212 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0232995 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 = 1.411900e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.440000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.909000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.441040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.450545e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.508650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.984293e+06 PMG: contraction number = , 7.984293e+06 NEWTON: attempting damping, relres = 1.049158e+04 NEWTON: attempting damping, relres = 6.121296e-01 NEWTON: attempting damping, relres = 7.907586e-01 NEWTON: damping accepted, relres = 6.121296e-01 PMG: iteration = 1 PMG: relative residual = 6.121296e-01 PMG: contraction number = 6.121296e-01 NEWTON: using errtol_s: 2.724310e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.572818e+06 PMG: contraction number = , 4.572818e+06 NEWTON: attempting damping, relres = 1.030139e-01 NEWTON: attempting damping, relres = 3.549128e-01 NEWTON: damping accepted, relres = 1.030139e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.030139e-01 PMG: contraction number = 1.682878e-01 NEWTON: using errtol_s: 4.584681e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.794240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.552226e+05 PMG: contraction number = , 6.552226e+05 PMG: iteration = 3 PMG: relative residual = 1.645694e-02 PMG: contraction number = 1.597545e-01 NEWTON: using errtol_s: 7.324236e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.913650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.156800e+05 PMG: contraction number = , 1.156800e+05 PMG: iteration = 4 PMG: relative residual = 3.403385e-03 PMG: contraction number = 2.068054e-01 NEWTON: using errtol_s: 1.514692e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.020020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.046582e+04 PMG: contraction number = , 3.046582e+04 PMG: iteration = 5 PMG: relative residual = 9.583276e-04 PMG: contraction number = 2.815807e-01 NEWTON: using errtol_s: 4.265080e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.108040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.011585e+04 PMG: contraction number = , 1.011585e+04 PMG: iteration = 6 PMG: relative residual = 3.049296e-04 PMG: contraction number = 3.181893e-01 NEWTON: using errtol_s: 1.357103e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.226870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.759765e+03 PMG: contraction number = , 3.759765e+03 PMG: iteration = 7 PMG: relative residual = 9.923851e-05 PMG: contraction number = 3.254473e-01 NEWTON: using errtol_s: 4.416654e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.359110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.347642e+03 PMG: contraction number = , 1.347642e+03 PMG: iteration = 8 PMG: relative residual = 2.983093e-05 PMG: contraction number = 3.005983e-01 NEWTON: using errtol_s: 1.327639e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.489250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.772221e+02 PMG: contraction number = , 4.772221e+02 PMG: iteration = 9 PMG: relative residual = 9.724585e-06 PMG: contraction number = 3.259900e-01 NEWTON: using errtol_s: 4.327970e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.589460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.976092e+02 PMG: contraction number = , 1.976092e+02 PMG: iteration = 10 PMG: relative residual = 3.998274e-06 PMG: contraction number = 4.111511e-01 NEWTON: using errtol_s: 1.779450e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.699840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.266223e+02 PMG: contraction number = , 1.266223e+02 PMG: iteration = 11 PMG: relative residual = 2.560607e-06 PMG: contraction number = 6.404280e-01 NEWTON: using errtol_s: 1.139609e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.786460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.973263e+01 PMG: contraction number = , 5.973263e+01 PMG: iteration = 12 PMG: relative residual = 1.207934e-06 PMG: contraction number = 4.717373e-01 NEWTON: using errtol_s: 5.375963e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.897300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.749116e+01 PMG: contraction number = , 2.749116e+01 PMG: iteration = 13 PMG: relative residual = 5.559334e-07 PMG: contraction number = 4.602350e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.558200e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.598860e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.213) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 8.025860473338E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.222068215276E+06 kT Vpmg_energy: dielEnergy = 1.110885750284E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.773000e+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 = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 22.9951) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, 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 = 4.860000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.800000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.331000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.224040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.835254e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.295670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.726343e+05 PMG: contraction number = , 6.726343e+05 NEWTON: attempting damping, relres = 8.943082e-02 NEWTON: attempting damping, relres = 5.420740e-01 NEWTON: damping accepted, relres = 8.943082e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 8.943082e-02 PMG: contraction number = 8.943082e-02 NEWTON: using errtol_s: 6.112823e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.422640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.968577e+04 PMG: contraction number = , 8.968577e+04 PMG: iteration = 2 PMG: relative residual = 1.181782e-02 PMG: contraction number = 1.321448e-01 NEWTON: using errtol_s: 8.077781e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.521170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.455142e+04 PMG: contraction number = , 1.455142e+04 PMG: iteration = 3 PMG: relative residual = 1.916029e-03 PMG: contraction number = 1.621305e-01 NEWTON: using errtol_s: 1.309654e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.621390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.647352e+03 PMG: contraction number = , 2.647352e+03 PMG: iteration = 4 PMG: relative residual = 3.485787e-04 PMG: contraction number = 1.819277e-01 NEWTON: using errtol_s: 2.382624e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.725950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.126683e+02 PMG: contraction number = , 5.126683e+02 PMG: iteration = 5 PMG: relative residual = 6.750337e-05 PMG: contraction number = 1.936532e-01 NEWTON: using errtol_s: 4.614027e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.823410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.111045e+02 PMG: contraction number = , 1.111045e+02 PMG: iteration = 6 PMG: relative residual = 1.462917e-05 PMG: contraction number = 2.167176e-01 NEWTON: using errtol_s: 9.999408e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.923100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.027653e+01 PMG: contraction number = , 3.027653e+01 PMG: iteration = 7 PMG: relative residual = 3.986534e-06 PMG: contraction number = 2.725059e-01 NEWTON: using errtol_s: 2.724897e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.029210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.061158e+01 PMG: contraction number = , 1.061158e+01 PMG: iteration = 8 PMG: relative residual = 1.397230e-06 PMG: contraction number = 3.504874e-01 NEWTON: using errtol_s: 9.550422e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.126060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.395646e+00 PMG: contraction number = , 4.395646e+00 PMG: iteration = 9 PMG: relative residual = 5.787776e-07 PMG: contraction number = 4.142321e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.605600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.005980e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.102) Vpmg_setPart: upper corner = (143.952, 160.29, 171.633) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.589381641985E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.353277561520E+05 kT Vpmg_energy: dielEnergy = 6.766083310586E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.955000e+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 = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 22.9951) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -79.484, -93.1155, -52.681 VPMG::focusFillBound -- New mesh maxs = 83.908, 87.4015, 111.213 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.102 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.633 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 = (-79.484, -93.1155, -52.681) VPMG::extEnergy Disj part upper corner = (83.908, 87.4015, 111.213) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.102) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.633) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000167058 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000237036 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 = 8.751000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.600000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.925000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.346260e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465340e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.415030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.338978e+06 PMG: contraction number = , 1.338978e+06 NEWTON: attempting damping, relres = 1.622298e-01 NEWTON: attempting damping, relres = 5.805623e-01 NEWTON: damping accepted, relres = 1.622298e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.622298e-01 PMG: contraction number = 1.622298e-01 NEWTON: using errtol_s: 1.211101e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.539970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.732517e+05 PMG: contraction number = , 1.732517e+05 PMG: iteration = 2 PMG: relative residual = 2.089435e-02 PMG: contraction number = 1.287948e-01 NEWTON: using errtol_s: 1.559834e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.638660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.567405e+04 PMG: contraction number = , 2.567405e+04 PMG: iteration = 3 PMG: relative residual = 3.095214e-03 PMG: contraction number = 1.481365e-01 NEWTON: using errtol_s: 2.310683e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.729000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.183344e+03 PMG: contraction number = , 4.183344e+03 PMG: iteration = 4 PMG: relative residual = 5.043329e-04 PMG: contraction number = 1.629396e-01 NEWTON: using errtol_s: 3.765017e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.838090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.302818e+02 PMG: contraction number = , 7.302818e+02 PMG: iteration = 5 PMG: relative residual = 8.804109e-05 PMG: contraction number = 1.745694e-01 NEWTON: using errtol_s: 6.572566e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.935780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.739218e+02 PMG: contraction number = , 1.739218e+02 PMG: iteration = 6 PMG: relative residual = 2.096754e-05 PMG: contraction number = 2.381563e-01 NEWTON: using errtol_s: 1.565298e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.034420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.194796e+01 PMG: contraction number = , 9.194796e+01 PMG: iteration = 7 PMG: relative residual = 1.108547e-05 PMG: contraction number = 5.286969e-01 NEWTON: using errtol_s: 8.275683e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.139310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.745871e+01 PMG: contraction number = , 3.745871e+01 PMG: iteration = 8 PMG: relative residual = 4.515929e-06 PMG: contraction number = 4.073736e-01 NEWTON: using errtol_s: 3.371294e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.231670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.833102e+01 PMG: contraction number = , 1.833102e+01 PMG: iteration = 9 PMG: relative residual = 2.210012e-06 PMG: contraction number = 4.893815e-01 NEWTON: using errtol_s: 1.649849e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.331650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.169215e+00 PMG: contraction number = , 8.169215e+00 PMG: iteration = 10 PMG: relative residual = 9.848579e-07 PMG: contraction number = 4.456346e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.049350e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.090660e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.213) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.508488923878E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.408617324062E+05 kT Vpmg_energy: dielEnergy = 1.704279355430E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.874000e+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 = 77.2861 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 57.702 Vpbe_ctor2: solute charge = -128 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (127.72, 144.845, 69.1678) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 14960229 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.338000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.440000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.918000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.645620e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.417195e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.716530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.772049e+06 PMG: contraction number = , 3.772049e+06 NEWTON: attempting damping, relres = 1.608604e+03 NEWTON: attempting damping, relres = 5.689815e-01 NEWTON: attempting damping, relres = 7.738062e-01 NEWTON: damping accepted, relres = 5.689815e-01 PMG: iteration = 1 PMG: relative residual = 5.689815e-01 PMG: contraction number = 5.689815e-01 NEWTON: using errtol_s: 1.944321e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.902570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.116981e+06 PMG: contraction number = , 2.116981e+06 NEWTON: attempting damping, relres = 6.231626e-02 NEWTON: attempting damping, relres = 3.125614e-01 NEWTON: damping accepted, relres = 6.231626e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 6.231626e-02 PMG: contraction number = 1.095225e-01 NEWTON: using errtol_s: 2.129468e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.020350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.978001e+05 PMG: contraction number = , 2.978001e+05 PMG: iteration = 3 PMG: relative residual = 9.398764e-03 PMG: contraction number = 1.508236e-01 NEWTON: using errtol_s: 3.211741e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.135240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.379925e+04 PMG: contraction number = , 5.379925e+04 PMG: iteration = 4 PMG: relative residual = 1.853578e-03 PMG: contraction number = 1.972151e-01 NEWTON: using errtol_s: 6.334039e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.267020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.223807e+04 PMG: contraction number = , 1.223807e+04 PMG: iteration = 5 PMG: relative residual = 4.339605e-04 PMG: contraction number = 2.341204e-01 NEWTON: using errtol_s: 1.482928e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.361680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.558107e+03 PMG: contraction number = , 3.558107e+03 PMG: iteration = 6 PMG: relative residual = 1.143720e-04 PMG: contraction number = 2.635539e-01 NEWTON: using errtol_s: 3.908314e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.468320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.197211e+03 PMG: contraction number = , 1.197211e+03 PMG: iteration = 7 PMG: relative residual = 3.362964e-05 PMG: contraction number = 2.940374e-01 NEWTON: using errtol_s: 1.149191e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.579280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.126587e+02 PMG: contraction number = , 4.126587e+02 PMG: iteration = 8 PMG: relative residual = 1.100067e-05 PMG: contraction number = 3.271124e-01 NEWTON: using errtol_s: 3.759144e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.678300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.397849e+02 PMG: contraction number = , 1.397849e+02 PMG: iteration = 9 PMG: relative residual = 3.691900e-06 PMG: contraction number = 3.356068e-01 NEWTON: using errtol_s: 1.261594e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.808650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.831372e+01 PMG: contraction number = , 4.831372e+01 PMG: iteration = 10 PMG: relative residual = 1.273435e-06 PMG: contraction number = 3.449268e-01 NEWTON: using errtol_s: 4.351578e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.896940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.669155e+01 PMG: contraction number = , 1.669155e+01 PMG: iteration = 11 PMG: relative residual = 4.397025e-07 PMG: contraction number = 3.452884e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.350690e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.391600e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.102) Vpmg_setPart: upper corner = (143.952, 160.29, 171.633) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 7.823988423330E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 7.848961973032E+05 kT Vpmg_energy: dielEnergy = 3.923006953156E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.007000e+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 = 77.2861 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 57.702 Vpbe_ctor2: solute charge = -128 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 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 2.77 max radius Vclist_setupGrid: Grid lengths = (127.72, 144.845, 69.1678) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 14960229 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 481, ny = 513, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 61 Vpmg_ctor2: PMG chose nf = 118688193, nc = 241865 Vpmg_ctor2: PMG chose narr = 135745564, narrc = 17057371 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1682972997, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -79.484, -93.1155, -52.681 VPMG::focusFillBound -- New mesh maxs = 83.908, 87.4015, 111.213 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.102 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.633 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.102) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.633) 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 = (-79.484, -93.1155, -52.681) VPMG::extEnergy Disj part upper corner = (83.908, 87.4015, 111.213) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.102) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.633) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0201824 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0232087 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 = 1.384000e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 6.600000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.961000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.211300e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.704010e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.282780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.646811e+06 PMG: contraction number = , 6.646811e+06 NEWTON: attempting damping, relres = 1.293607e+04 NEWTON: attempting damping, relres = 6.186928e-01 NEWTON: attempting damping, relres = 7.908672e-01 NEWTON: damping accepted, relres = 6.186928e-01 PMG: iteration = 1 PMG: relative residual = 6.186928e-01 PMG: contraction number = 6.186928e-01 NEWTON: using errtol_s: 2.291644e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.442720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.816464e+06 PMG: contraction number = , 3.816464e+06 NEWTON: attempting damping, relres = 1.054442e-01 NEWTON: attempting damping, relres = 3.588855e-01 NEWTON: damping accepted, relres = 1.054442e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.054442e-01 PMG: contraction number = 1.704306e-01 NEWTON: using errtol_s: 3.905664e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.572250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.574443e+05 PMG: contraction number = , 5.574443e+05 PMG: iteration = 3 PMG: relative residual = 1.744931e-02 PMG: contraction number = 1.654838e-01 NEWTON: using errtol_s: 6.463241e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.677290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.018026e+05 PMG: contraction number = , 1.018026e+05 PMG: iteration = 4 PMG: relative residual = 3.770178e-03 PMG: contraction number = 2.160646e-01 NEWTON: using errtol_s: 1.396478e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.769520e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.843039e+04 PMG: contraction number = , 2.843039e+04 PMG: iteration = 5 PMG: relative residual = 1.108185e-03 PMG: contraction number = 2.939343e-01 NEWTON: using errtol_s: 4.104726e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.861440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.799555e+03 PMG: contraction number = , 9.799555e+03 PMG: iteration = 6 PMG: relative residual = 3.607001e-04 PMG: contraction number = 3.254874e-01 NEWTON: using errtol_s: 1.336037e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.963550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.672347e+03 PMG: contraction number = , 3.672347e+03 PMG: iteration = 7 PMG: relative residual = 1.177634e-04 PMG: contraction number = 3.264857e-01 NEWTON: using errtol_s: 4.361969e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.058020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.311927e+03 PMG: contraction number = , 1.311927e+03 PMG: iteration = 8 PMG: relative residual = 3.511112e-05 PMG: contraction number = 2.981496e-01 NEWTON: using errtol_s: 1.300519e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.160300e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.573845e+02 PMG: contraction number = , 4.573845e+02 PMG: iteration = 9 PMG: relative residual = 1.120805e-05 PMG: contraction number = 3.192166e-01 NEWTON: using errtol_s: 4.151474e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.249960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.817536e+02 PMG: contraction number = , 1.817536e+02 PMG: iteration = 10 PMG: relative residual = 4.419080e-06 PMG: contraction number = 3.942771e-01 NEWTON: using errtol_s: 1.636831e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.352390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.113257e+02 PMG: contraction number = , 1.113257e+02 PMG: iteration = 11 PMG: relative residual = 2.705025e-06 PMG: contraction number = 6.121240e-01 NEWTON: using errtol_s: 1.001944e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.447790e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.664656e+01 PMG: contraction number = , 5.664656e+01 PMG: iteration = 12 PMG: relative residual = 1.376401e-06 PMG: contraction number = 5.088311e-01 NEWTON: using errtol_s: 5.098201e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.548180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.457546e+01 PMG: contraction number = , 2.457546e+01 PMG: iteration = 13 PMG: relative residual = 5.971347e-07 PMG: contraction number = 4.338379e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.401680e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.444240e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.213) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.213) 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 full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 7.778259223068E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.881208641405E+06 kT Vpmg_energy: dielEnergy = 9.404587858404E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.821000e+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. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.748270e+03