############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Mar 17 11:05:23 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_allh40.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb40.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, 86.287) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 29.303) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 86.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 30.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 58.26) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Mon Mar 17 11:06:17 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_allh40.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb40.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, 86.287) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 29.303) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 86.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 30.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 58.26) 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 29.303 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.3416 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575488 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 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.763 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.157 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.287 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 111.287 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 29.303 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.3416 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575488 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 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.763 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.157 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.287 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 111.287 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 29.303 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.593583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.3416 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.575488 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 29.303 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 171.763 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -113.157 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 111.287 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 111.287 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 = 88.8629 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 116.715 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, 128.296) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 10796025 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 = 8.029000e+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 = 6.460000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.926000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228200e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.100043e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.928100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.440468e+06 PMG: contraction number = , 4.440468e+06 NEWTON: attempting damping, relres = 1.172664e+03 NEWTON: attempting damping, relres = 5.636817e-01 NEWTON: attempting damping, relres = 7.732923e-01 NEWTON: damping accepted, relres = 5.636817e-01 PMG: iteration = 1 PMG: relative residual = 5.636817e-01 PMG: contraction number = 5.636817e-01 NEWTON: using errtol_s: 2.311119e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.551300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.491517e+06 PMG: contraction number = , 2.491517e+06 NEWTON: attempting damping, relres = 5.992273e-02 NEWTON: attempting damping, relres = 3.091214e-01 NEWTON: damping accepted, relres = 5.992273e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 5.992273e-02 PMG: contraction number = 1.063060e-01 NEWTON: using errtol_s: 2.456858e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.806700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.491376e+05 PMG: contraction number = , 3.491376e+05 PMG: iteration = 3 PMG: relative residual = 8.840715e-03 PMG: contraction number = 1.475353e-01 NEWTON: using errtol_s: 3.624731e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.682300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.193491e+04 PMG: contraction number = , 6.193491e+04 PMG: iteration = 4 PMG: relative residual = 1.682181e-03 PMG: contraction number = 1.902766e-01 NEWTON: using errtol_s: 6.897014e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.615400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.356139e+04 PMG: contraction number = , 1.356139e+04 PMG: iteration = 5 PMG: relative residual = 3.776245e-04 PMG: contraction number = 2.244850e-01 NEWTON: using errtol_s: 1.548277e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.549400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.762247e+03 PMG: contraction number = , 3.762247e+03 PMG: iteration = 6 PMG: relative residual = 9.645481e-05 PMG: contraction number = 2.554252e-01 NEWTON: using errtol_s: 3.954689e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.430200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.229449e+03 PMG: contraction number = , 1.229449e+03 PMG: iteration = 7 PMG: relative residual = 2.823502e-05 PMG: contraction number = 2.927279e-01 NEWTON: using errtol_s: 1.157648e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.362100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.202248e+02 PMG: contraction number = , 4.202248e+02 PMG: iteration = 8 PMG: relative residual = 9.295535e-06 PMG: contraction number = 3.292201e-01 NEWTON: using errtol_s: 3.811209e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.446250e+02 PMG: contraction number = , 1.446250e+02 PMG: iteration = 9 PMG: relative residual = 3.180003e-06 PMG: contraction number = 3.421001e-01 NEWTON: using errtol_s: 1.303815e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.127940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.170628e+01 PMG: contraction number = , 5.170628e+01 PMG: iteration = 10 PMG: relative residual = 1.135506e-06 PMG: contraction number = 3.570770e-01 NEWTON: using errtol_s: 4.655623e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.913077e+01 PMG: contraction number = , 1.913077e+01 PMG: iteration = 11 PMG: relative residual = 4.199841e-07 PMG: contraction number = 3.698652e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.167950e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.209310e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.157) Vpmg_setPart: upper corner = (143.952, 160.29, 171.763) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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 = 8.075269282742E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.197884811532E+05 kT Vpmg_energy: dielEnergy = 4.597440026406E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.830000e+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 = 88.8629 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 116.715 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, 128.296) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 10796025 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, 111.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.157 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.763 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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, 111.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.157) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.763) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0200586 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0232275 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 = 1.544600e+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 = 6.430000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.939000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.516950e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.450541e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.587900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.984211e+06 PMG: contraction number = , 7.984211e+06 NEWTON: attempting damping, relres = 1.030890e+04 NEWTON: attempting damping, relres = 6.120719e-01 NEWTON: attempting damping, relres = 7.907581e-01 NEWTON: damping accepted, relres = 6.120719e-01 PMG: iteration = 1 PMG: relative residual = 6.120719e-01 PMG: contraction number = 6.120719e-01 NEWTON: using errtol_s: 2.724051e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.765970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.573631e+06 PMG: contraction number = , 4.573631e+06 NEWTON: attempting damping, relres = 1.030195e-01 NEWTON: attempting damping, relres = 3.548851e-01 NEWTON: damping accepted, relres = 1.030195e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.030195e-01 PMG: contraction number = 1.683128e-01 NEWTON: using errtol_s: 4.584925e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.523322e+05 PMG: contraction number = , 6.523322e+05 PMG: iteration = 3 PMG: relative residual = 1.639530e-02 PMG: contraction number = 1.591476e-01 NEWTON: using errtol_s: 7.296797e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.004270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.148016e+05 PMG: contraction number = , 1.148016e+05 PMG: iteration = 4 PMG: relative residual = 3.384237e-03 PMG: contraction number = 2.064150e-01 NEWTON: using errtol_s: 1.506168e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.110540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.998428e+04 PMG: contraction number = , 2.998428e+04 PMG: iteration = 5 PMG: relative residual = 9.478073e-04 PMG: contraction number = 2.800653e-01 NEWTON: using errtol_s: 4.218255e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.197490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.931491e+03 PMG: contraction number = , 9.931491e+03 PMG: iteration = 6 PMG: relative residual = 3.005625e-04 PMG: contraction number = 3.171136e-01 NEWTON: using errtol_s: 1.337666e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.307060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.700463e+03 PMG: contraction number = , 3.700463e+03 PMG: iteration = 7 PMG: relative residual = 9.771783e-05 PMG: contraction number = 3.251165e-01 NEWTON: using errtol_s: 4.348972e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.408840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.333763e+03 PMG: contraction number = , 1.333763e+03 PMG: iteration = 8 PMG: relative residual = 2.940171e-05 PMG: contraction number = 3.008837e-01 NEWTON: using errtol_s: 1.308535e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.520350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.712166e+02 PMG: contraction number = , 4.712166e+02 PMG: iteration = 9 PMG: relative residual = 9.596391e-06 PMG: contraction number = 3.263889e-01 NEWTON: using errtol_s: 4.270913e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.630980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.924108e+02 PMG: contraction number = , 1.924108e+02 PMG: iteration = 10 PMG: relative residual = 3.893133e-06 PMG: contraction number = 4.056872e-01 NEWTON: using errtol_s: 1.732655e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.724590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.200053e+02 PMG: contraction number = , 1.200053e+02 PMG: iteration = 11 PMG: relative residual = 2.426796e-06 PMG: contraction number = 6.233530e-01 NEWTON: using errtol_s: 1.080056e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.827580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.097198e+01 PMG: contraction number = , 6.097198e+01 PMG: iteration = 12 PMG: relative residual = 1.232997e-06 PMG: contraction number = 5.080760e-01 NEWTON: using errtol_s: 5.487504e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.924580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.727133e+01 PMG: contraction number = , 2.727133e+01 PMG: iteration = 13 PMG: relative residual = 5.514883e-07 PMG: contraction number = 4.472746e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.470550e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.511790e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.287) 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 = 8.025545971518E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.221767921018E+06 kT Vpmg_energy: dielEnergy = 1.110735684135E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.766000e+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, 23.0691) 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 = 4.862000e+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 = 6.420000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 3.037000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.213500e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.834937e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.288780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.721168e+05 PMG: contraction number = , 6.721168e+05 NEWTON: attempting damping, relres = 8.936629e-02 NEWTON: attempting damping, relres = 5.420499e-01 NEWTON: damping accepted, relres = 8.936629e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 8.936629e-02 PMG: contraction number = 8.936629e-02 NEWTON: using errtol_s: 6.108129e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.430020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.958633e+04 PMG: contraction number = , 8.958633e+04 PMG: iteration = 2 PMG: relative residual = 1.180543e-02 PMG: contraction number = 1.321017e-01 NEWTON: using errtol_s: 8.068940e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.515980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.454639e+04 PMG: contraction number = , 1.454639e+04 PMG: iteration = 3 PMG: relative residual = 1.915456e-03 PMG: contraction number = 1.622520e-01 NEWTON: using errtol_s: 1.309202e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.603740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.660666e+03 PMG: contraction number = , 2.660666e+03 PMG: iteration = 4 PMG: relative residual = 3.503481e-04 PMG: contraction number = 1.829059e-01 NEWTON: using errtol_s: 2.394607e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.690650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.230147e+02 PMG: contraction number = , 5.230147e+02 PMG: iteration = 5 PMG: relative residual = 6.886888e-05 PMG: contraction number = 1.965727e-01 NEWTON: using errtol_s: 4.707145e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.777590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.168402e+02 PMG: contraction number = , 1.168402e+02 PMG: iteration = 6 PMG: relative residual = 1.538511e-05 PMG: contraction number = 2.233972e-01 NEWTON: using errtol_s: 1.051563e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.865550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.291250e+01 PMG: contraction number = , 3.291250e+01 PMG: iteration = 7 PMG: relative residual = 4.333816e-06 PMG: contraction number = 2.816889e-01 NEWTON: using errtol_s: 2.962136e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.960670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.177781e+01 PMG: contraction number = , 1.177781e+01 PMG: iteration = 8 PMG: relative residual = 1.550860e-06 PMG: contraction number = 3.578508e-01 NEWTON: using errtol_s: 1.060003e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.886781e+00 PMG: contraction number = , 4.886781e+00 PMG: iteration = 9 PMG: relative residual = 6.434756e-07 PMG: contraction number = 4.149154e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.886400e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.309200e+02 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.157) Vpmg_setPart: upper corner = (143.952, 160.29, 171.763) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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 = 2.589195158232E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.352429798361E+05 kT Vpmg_energy: dielEnergy = 6.761844561491E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.992000e+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, 23.0691) 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, 111.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.157 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.763 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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, 111.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.157) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.763) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.00016665 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000236387 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 = 9.284000e+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 = 6.490000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.915000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.267920e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465430e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.338450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.339260e+06 PMG: contraction number = , 1.339260e+06 NEWTON: attempting damping, relres = 1.622639e-01 NEWTON: attempting damping, relres = 5.805773e-01 NEWTON: damping accepted, relres = 1.622639e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.622639e-01 PMG: contraction number = 1.622639e-01 NEWTON: using errtol_s: 1.211369e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.456070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.733925e+05 PMG: contraction number = , 1.733925e+05 PMG: iteration = 2 PMG: relative residual = 2.091118e-02 PMG: contraction number = 1.288714e-01 NEWTON: using errtol_s: 1.561109e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.541170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.573778e+04 PMG: contraction number = , 2.573778e+04 PMG: iteration = 3 PMG: relative residual = 3.102859e-03 PMG: contraction number = 1.483828e-01 NEWTON: using errtol_s: 2.316418e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.625850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.201044e+03 PMG: contraction number = , 4.201044e+03 PMG: iteration = 4 PMG: relative residual = 5.064607e-04 PMG: contraction number = 1.632239e-01 NEWTON: using errtol_s: 3.780947e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.710500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.327695e+02 PMG: contraction number = , 7.327695e+02 PMG: iteration = 5 PMG: relative residual = 8.833991e-05 PMG: contraction number = 1.744260e-01 NEWTON: using errtol_s: 6.594954e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.799390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.713422e+02 PMG: contraction number = , 1.713422e+02 PMG: iteration = 6 PMG: relative residual = 2.065630e-05 PMG: contraction number = 2.338275e-01 NEWTON: using errtol_s: 1.542082e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.937320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.017219e+01 PMG: contraction number = , 9.017219e+01 PMG: iteration = 7 PMG: relative residual = 1.087123e-05 PMG: contraction number = 5.262910e-01 NEWTON: using errtol_s: 8.115837e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.051000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.783214e+01 PMG: contraction number = , 3.783214e+01 PMG: iteration = 8 PMG: relative residual = 4.560894e-06 PMG: contraction number = 4.195381e-01 NEWTON: using errtol_s: 3.404903e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.149810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.820298e+01 PMG: contraction number = , 1.820298e+01 PMG: iteration = 9 PMG: relative residual = 2.194551e-06 PMG: contraction number = 4.811668e-01 NEWTON: using errtol_s: 1.638326e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.234020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.230277e+00 PMG: contraction number = , 8.230277e+00 PMG: iteration = 10 PMG: relative residual = 9.922075e-07 PMG: contraction number = 4.521233e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.020950e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.061930e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.287) 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 = 2.509444557647E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.407953889988E+05 kT Vpmg_energy: dielEnergy = 1.703947621794E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.884000e+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 = 7.439000e+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 = 6.610000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.915000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.529920e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.416967e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.602150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.770578e+06 PMG: contraction number = , 3.770578e+06 NEWTON: attempting damping, relres = 1.510513e+03 NEWTON: attempting damping, relres = 5.682982e-01 NEWTON: attempting damping, relres = 7.737931e-01 NEWTON: damping accepted, relres = 5.682982e-01 PMG: iteration = 1 PMG: relative residual = 5.682982e-01 PMG: contraction number = 5.682982e-01 NEWTON: using errtol_s: 1.941856e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.758270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.115496e+06 PMG: contraction number = , 2.115496e+06 NEWTON: attempting damping, relres = 6.201976e-02 NEWTON: attempting damping, relres = 3.121299e-01 NEWTON: damping accepted, relres = 6.201976e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 6.201976e-02 PMG: contraction number = 1.091324e-01 NEWTON: using errtol_s: 2.119195e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.884750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.973724e+05 PMG: contraction number = , 2.973724e+05 PMG: iteration = 3 PMG: relative residual = 9.294212e-03 PMG: contraction number = 1.498589e-01 NEWTON: using errtol_s: 3.175801e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.973950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.361967e+04 PMG: contraction number = , 5.361967e+04 PMG: iteration = 4 PMG: relative residual = 1.816549e-03 PMG: contraction number = 1.954495e-01 NEWTON: using errtol_s: 6.207089e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.068310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.210810e+04 PMG: contraction number = , 1.210810e+04 PMG: iteration = 5 PMG: relative residual = 4.201835e-04 PMG: contraction number = 2.313086e-01 NEWTON: using errtol_s: 1.435753e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.163310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.495725e+03 PMG: contraction number = , 3.495725e+03 PMG: iteration = 6 PMG: relative residual = 1.100165e-04 PMG: contraction number = 2.618298e-01 NEWTON: using errtol_s: 3.759229e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.261600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.164247e+03 PMG: contraction number = , 1.164247e+03 PMG: iteration = 7 PMG: relative residual = 3.233834e-05 PMG: contraction number = 2.939407e-01 NEWTON: using errtol_s: 1.104990e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.369580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.002212e+02 PMG: contraction number = , 4.002212e+02 PMG: iteration = 8 PMG: relative residual = 1.063904e-05 PMG: contraction number = 3.289914e-01 NEWTON: using errtol_s: 3.635324e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.460340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.363873e+02 PMG: contraction number = , 1.363873e+02 PMG: iteration = 9 PMG: relative residual = 3.599672e-06 PMG: contraction number = 3.383456e-01 NEWTON: using errtol_s: 1.229996e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.556970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.810815e+01 PMG: contraction number = , 4.810815e+01 PMG: iteration = 10 PMG: relative residual = 1.267824e-06 PMG: contraction number = 3.522055e-01 NEWTON: using errtol_s: 4.332113e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.727062e+01 PMG: contraction number = , 1.727062e+01 PMG: iteration = 11 PMG: relative residual = 4.549576e-07 PMG: contraction number = 3.588491e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.187970e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.229800e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -113.157) Vpmg_setPart: upper corner = (143.952, 160.29, 171.763) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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 = 7.823201320768E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 7.845476586635E+05 kT Vpmg_energy: dielEnergy = 3.921264756330E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.879000e+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, 111.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -113.157 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 171.763 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -113.157) Vpmg_setPart: actual maxima = (143.952, 160.29, 171.763) 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, 111.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -113.157) VPMG::extEnergy Old upper corner = (143.952, 160.29, 171.763) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0201171 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0231352 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 = 1.320400e+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 = 6.500000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.963000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.924260e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.703997e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.992210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.646449e+06 PMG: contraction number = , 6.646449e+06 NEWTON: attempting damping, relres = 1.271217e+04 NEWTON: attempting damping, relres = 6.186264e-01 NEWTON: attempting damping, relres = 7.908653e-01 NEWTON: damping accepted, relres = 6.186264e-01 PMG: iteration = 1 PMG: relative residual = 6.186264e-01 PMG: contraction number = 6.186264e-01 NEWTON: using errtol_s: 2.291390e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.148190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.816705e+06 PMG: contraction number = , 3.816705e+06 NEWTON: attempting damping, relres = 1.054454e-01 NEWTON: attempting damping, relres = 3.588542e-01 NEWTON: damping accepted, relres = 1.054454e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.054454e-01 PMG: contraction number = 1.704509e-01 NEWTON: using errtol_s: 3.905696e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.268870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.564179e+05 PMG: contraction number = , 5.564179e+05 PMG: iteration = 3 PMG: relative residual = 1.741990e-02 PMG: contraction number = 1.652030e-01 NEWTON: using errtol_s: 6.452327e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.357210e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.013842e+05 PMG: contraction number = , 1.013842e+05 PMG: iteration = 4 PMG: relative residual = 3.758490e-03 PMG: contraction number = 2.157584e-01 NEWTON: using errtol_s: 1.392143e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.445470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.820374e+04 PMG: contraction number = , 2.820374e+04 PMG: iteration = 5 PMG: relative residual = 1.101746e-03 PMG: contraction number = 2.931352e-01 NEWTON: using errtol_s: 4.080863e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.533090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.711531e+03 PMG: contraction number = , 9.711531e+03 PMG: iteration = 6 PMG: relative residual = 3.578014e-04 PMG: contraction number = 3.247586e-01 NEWTON: using errtol_s: 1.325295e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.621840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.643013e+03 PMG: contraction number = , 3.643013e+03 PMG: iteration = 7 PMG: relative residual = 1.166675e-04 PMG: contraction number = 3.260677e-01 NEWTON: using errtol_s: 4.321361e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.710360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.306289e+03 PMG: contraction number = , 1.306289e+03 PMG: iteration = 8 PMG: relative residual = 3.479419e-05 PMG: contraction number = 2.982337e-01 NEWTON: using errtol_s: 1.288776e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.798240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.543075e+02 PMG: contraction number = , 4.543075e+02 PMG: iteration = 9 PMG: relative residual = 1.112486e-05 PMG: contraction number = 3.197332e-01 NEWTON: using errtol_s: 4.120644e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886930e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.782276e+02 PMG: contraction number = , 1.782276e+02 PMG: iteration = 10 PMG: relative residual = 4.333420e-06 PMG: contraction number = 3.895259e-01 NEWTON: using errtol_s: 1.605098e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.975100e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.058926e+02 PMG: contraction number = , 1.058926e+02 PMG: iteration = 11 PMG: relative residual = 2.573019e-06 PMG: contraction number = 5.937617e-01 NEWTON: using errtol_s: 9.530455e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.081340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.743521e+01 PMG: contraction number = , 5.743521e+01 PMG: iteration = 12 PMG: relative residual = 1.395568e-06 PMG: contraction number = 5.423853e-01 NEWTON: using errtol_s: 5.169179e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.169530e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.466921e+01 PMG: contraction number = , 2.466921e+01 PMG: iteration = 13 PMG: relative residual = 5.994148e-07 PMG: contraction number = 4.295132e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.303070e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.344850e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 111.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 111.287) 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 = 7.778301263460E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.880974671693E+06 kT Vpmg_energy: dielEnergy = 9.403418761061E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.828000e+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 = 8.358520e+03