############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Mar 14 16:25:34 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.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, 449) 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, 449) 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, 449) 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, 81.287) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 26.803) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Mar 14 16:27:30 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_allh35.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb35.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, 449) 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, 449) 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, 449) 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, 81.287) Valist_getStatistics: Min atom coordinate: (-54.484, -68.116, -27.681) Valist_getStatistics: Molecule center: (2.212, -2.8575, 26.803) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 81.287) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 25.233) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 53.26) 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 26.803 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.60808 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.354839 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.58354 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 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 163.013 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -109.407 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 106.287 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 106.287 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 26.803 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.60808 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.354839 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.58354 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 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 163.013 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -109.407 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 106.287 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 106.287 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 26.803 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 2.212 -2.857 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.590583, 0.637291, 0.60808 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.3404, 0.352572, 0.354839 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.576379, 0.553236, 0.58354 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 26.803 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 143.952 160.29 163.013 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -139.528 -166.004 -109.407 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 83.908 87.4015 106.287 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 106.287 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 = 87.375 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 111.715 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, 123.296) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 11116976 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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, 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 = 8.462000e+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 = 6.360000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 4.540000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.441000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.089529e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.099500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.359290e+06 PMG: contraction number = , 4.359290e+06 NEWTON: attempting damping, relres = 1.925080e+03 NEWTON: attempting damping, relres = 5.666528e-01 NEWTON: attempting damping, relres = 7.729281e-01 NEWTON: damping accepted, relres = 5.666528e-01 PMG: iteration = 1 PMG: relative residual = 5.666528e-01 PMG: contraction number = 5.666528e-01 NEWTON: using errtol_s: 2.317343e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.661400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.444054e+06 PMG: contraction number = , 2.444054e+06 NEWTON: attempting damping, relres = 6.028357e-02 NEWTON: attempting damping, relres = 3.104973e-01 NEWTON: damping accepted, relres = 6.028357e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 6.028357e-02 PMG: contraction number = 1.063854e-01 NEWTON: using errtol_s: 2.465314e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.973100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.389755e+05 PMG: contraction number = , 3.389755e+05 PMG: iteration = 3 PMG: relative residual = 9.057289e-03 PMG: contraction number = 1.502447e-01 NEWTON: using errtol_s: 3.704005e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.855900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.982506e+04 PMG: contraction number = , 5.982506e+04 PMG: iteration = 4 PMG: relative residual = 1.785228e-03 PMG: contraction number = 1.971040e-01 NEWTON: using errtol_s: 7.300743e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.738000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.303671e+04 PMG: contraction number = , 1.303671e+04 PMG: iteration = 5 PMG: relative residual = 4.154587e-04 PMG: contraction number = 2.327202e-01 NEWTON: using errtol_s: 1.699030e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.616600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.728598e+03 PMG: contraction number = , 3.728598e+03 PMG: iteration = 6 PMG: relative residual = 1.088941e-04 PMG: contraction number = 2.621058e-01 NEWTON: using errtol_s: 4.453257e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.635600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.271669e+03 PMG: contraction number = , 1.271669e+03 PMG: iteration = 7 PMG: relative residual = 3.118819e-05 PMG: contraction number = 2.864084e-01 NEWTON: using errtol_s: 1.275450e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.526200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.336277e+02 PMG: contraction number = , 4.336277e+02 PMG: iteration = 8 PMG: relative residual = 9.731767e-06 PMG: contraction number = 3.120338e-01 NEWTON: using errtol_s: 3.979835e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.436689e+02 PMG: contraction number = , 1.436689e+02 PMG: iteration = 9 PMG: relative residual = 3.171859e-06 PMG: contraction number = 3.259284e-01 NEWTON: using errtol_s: 1.297141e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.142990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.751390e+01 PMG: contraction number = , 4.751390e+01 PMG: iteration = 10 PMG: relative residual = 1.046407e-06 PMG: contraction number = 3.299035e-01 NEWTON: using errtol_s: 4.279313e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.535178e+01 PMG: contraction number = , 1.535178e+01 PMG: iteration = 11 PMG: relative residual = 3.379045e-07 PMG: contraction number = 3.229187e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.146420e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.204750e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -109.407) Vpmg_setPart: upper corner = (143.952, 160.29, 163.013) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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 = 8.126065857621E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.057113823518E+05 kT Vpmg_energy: dielEnergy = 4.527039933992E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.852000e+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 = 87.375 Vpbe_ctor2: solute dimensions = 116.072 x 133.197 x 111.715 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, 123.296) Vclist_setupGrid: Grid lower corner = (-61.6479, -75.2799, -34.8449) Vclist_assignAtoms: Have 11116976 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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, 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, 106.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -109.407 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 163.013 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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, 106.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -109.407) VPMG::extEnergy Old upper corner = (143.952, 160.29, 163.013) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0192012 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0221446 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 = 1.467900e+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 = 6.060000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.698000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.509470e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.449400e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.575690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.912536e+06 PMG: contraction number = , 7.912536e+06 NEWTON: attempting damping, relres = 1.314196e+04 NEWTON: attempting damping, relres = 6.149283e-01 NEWTON: attempting damping, relres = 7.904204e-01 NEWTON: damping accepted, relres = 6.149283e-01 PMG: iteration = 1 PMG: relative residual = 6.149283e-01 PMG: contraction number = 6.149283e-01 NEWTON: using errtol_s: 2.736062e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.739630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.535209e+06 PMG: contraction number = , 4.535209e+06 NEWTON: attempting damping, relres = 1.034261e-01 NEWTON: attempting damping, relres = 3.562528e-01 NEWTON: damping accepted, relres = 1.034261e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.034261e-01 PMG: contraction number = 1.681920e-01 NEWTON: using errtol_s: 4.601839e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.870470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.539128e+05 PMG: contraction number = , 6.539128e+05 PMG: iteration = 3 PMG: relative residual = 1.684425e-02 PMG: contraction number = 1.628628e-01 NEWTON: using errtol_s: 7.494683e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.958540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.169094e+05 PMG: contraction number = , 1.169094e+05 PMG: iteration = 4 PMG: relative residual = 3.578846e-03 PMG: contraction number = 2.124669e-01 NEWTON: using errtol_s: 1.592372e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.049600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.101336e+04 PMG: contraction number = , 3.101336e+04 PMG: iteration = 5 PMG: relative residual = 1.021369e-03 PMG: contraction number = 2.853905e-01 NEWTON: using errtol_s: 4.544479e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.151190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.066078e+04 PMG: contraction number = , 1.066078e+04 PMG: iteration = 6 PMG: relative residual = 3.326355e-04 PMG: contraction number = 3.256761e-01 NEWTON: using errtol_s: 1.480028e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.242770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.139986e+03 PMG: contraction number = , 4.139986e+03 PMG: iteration = 7 PMG: relative residual = 1.119720e-04 PMG: contraction number = 3.366209e-01 NEWTON: using errtol_s: 4.982084e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.332840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.544695e+03 PMG: contraction number = , 1.544695e+03 PMG: iteration = 8 PMG: relative residual = 3.482751e-05 PMG: contraction number = 3.110375e-01 NEWTON: using errtol_s: 1.549615e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.429200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.545590e+02 PMG: contraction number = , 5.545590e+02 PMG: iteration = 9 PMG: relative residual = 1.133375e-05 PMG: contraction number = 3.254252e-01 NEWTON: using errtol_s: 5.042839e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.526290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.114640e+02 PMG: contraction number = , 2.114640e+02 PMG: iteration = 10 PMG: relative residual = 4.280419e-06 PMG: contraction number = 3.776702e-01 NEWTON: using errtol_s: 1.904530e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.616010e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.118788e+02 PMG: contraction number = , 1.118788e+02 PMG: iteration = 11 PMG: relative residual = 2.263084e-06 PMG: contraction number = 5.287061e-01 NEWTON: using errtol_s: 1.006937e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.703890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.936846e+01 PMG: contraction number = , 6.936846e+01 PMG: iteration = 12 PMG: relative residual = 1.403153e-06 PMG: contraction number = 6.200181e-01 NEWTON: using errtol_s: 6.243189e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.794410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.952877e+01 PMG: contraction number = , 2.952877e+01 PMG: iteration = 13 PMG: relative residual = 5.972920e-07 PMG: contraction number = 4.256785e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.350590e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.389940e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 106.287) 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 = 8.075630873403E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.183462713468E+06 kT Vpmg_energy: dielEnergy = 1.091582091217E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.449000e+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, 18.0691) 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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.357000e+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 = 6.010000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.692000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074280e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.810522e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.136640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.587809e+05 PMG: contraction number = , 6.587809e+05 NEWTON: attempting damping, relres = 8.791305e-02 NEWTON: attempting damping, relres = 5.412967e-01 NEWTON: damping accepted, relres = 8.791305e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 8.791305e-02 PMG: contraction number = 8.791305e-02 NEWTON: using errtol_s: 5.987338e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.245840e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.726107e+04 PMG: contraction number = , 8.726107e+04 PMG: iteration = 2 PMG: relative residual = 1.153913e-02 PMG: contraction number = 1.312561e-01 NEWTON: using errtol_s: 7.858749e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.329260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.402376e+04 PMG: contraction number = , 1.402376e+04 PMG: iteration = 3 PMG: relative residual = 1.853267e-03 PMG: contraction number = 1.606072e-01 NEWTON: using errtol_s: 1.262171e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.408580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.526136e+03 PMG: contraction number = , 2.526136e+03 PMG: iteration = 4 PMG: relative residual = 3.338261e-04 PMG: contraction number = 1.801285e-01 NEWTON: using errtol_s: 2.273530e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.540110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.893590e+02 PMG: contraction number = , 4.893590e+02 PMG: iteration = 5 PMG: relative residual = 6.466838e-05 PMG: contraction number = 1.937188e-01 NEWTON: using errtol_s: 4.404255e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.628390e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.099947e+02 PMG: contraction number = , 1.099947e+02 PMG: iteration = 6 PMG: relative residual = 1.453564e-05 PMG: contraction number = 2.247720e-01 NEWTON: using errtol_s: 9.899531e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.707670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.201010e+01 PMG: contraction number = , 3.201010e+01 PMG: iteration = 7 PMG: relative residual = 4.230116e-06 PMG: contraction number = 2.910168e-01 NEWTON: using errtol_s: 2.880930e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.836040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.217919e+01 PMG: contraction number = , 1.217919e+01 PMG: iteration = 8 PMG: relative residual = 1.609461e-06 PMG: contraction number = 3.804769e-01 NEWTON: using errtol_s: 1.096127e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.960140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.238962e+00 PMG: contraction number = , 5.238962e+00 PMG: iteration = 9 PMG: relative residual = 6.923238e-07 PMG: contraction number = 4.301587e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.379600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.768000e+02 Vpmg_setPart: lower corner = (-139.528, -166.004, -109.407) Vpmg_setPart: upper corner = (143.952, 160.29, 163.013) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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 = 2.592975617118E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.329593083132E+05 kT Vpmg_energy: dielEnergy = 6.647660494826E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.871000e+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, 18.0691) 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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, 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, 106.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -109.407 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 163.013 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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, 106.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -109.407) VPMG::extEnergy Old upper corner = (143.952, 160.29, 163.013) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000156841 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.00022194 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 = 8.436000e+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 = 6.200000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.694000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.169160e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.463685e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.234560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.330343e+06 PMG: contraction number = , 1.330343e+06 NEWTON: attempting damping, relres = 1.612320e-01 NEWTON: attempting damping, relres = 5.800523e-01 NEWTON: damping accepted, relres = 1.612320e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.612320e-01 PMG: contraction number = 1.612320e-01 NEWTON: using errtol_s: 1.203385e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.358550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.729036e+05 PMG: contraction number = , 1.729036e+05 PMG: iteration = 2 PMG: relative residual = 2.085671e-02 PMG: contraction number = 1.293583e-01 NEWTON: using errtol_s: 1.556679e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.449650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.574750e+04 PMG: contraction number = , 2.574750e+04 PMG: iteration = 3 PMG: relative residual = 3.104756e-03 PMG: contraction number = 1.488612e-01 NEWTON: using errtol_s: 2.317292e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.539870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.214771e+03 PMG: contraction number = , 4.214771e+03 PMG: iteration = 4 PMG: relative residual = 5.082345e-04 PMG: contraction number = 1.636955e-01 NEWTON: using errtol_s: 3.793302e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.630640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.473435e+02 PMG: contraction number = , 7.473435e+02 PMG: iteration = 5 PMG: relative residual = 9.011815e-05 PMG: contraction number = 1.773161e-01 NEWTON: using errtol_s: 6.726134e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.721810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.983538e+02 PMG: contraction number = , 1.983538e+02 PMG: iteration = 6 PMG: relative residual = 2.391831e-05 PMG: contraction number = 2.654106e-01 NEWTON: using errtol_s: 1.785188e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.812950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.102808e+02 PMG: contraction number = , 1.102808e+02 PMG: iteration = 7 PMG: relative residual = 1.329888e-05 PMG: contraction number = 5.560126e-01 NEWTON: using errtol_s: 9.925868e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.904110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.472163e+01 PMG: contraction number = , 4.472163e+01 PMG: iteration = 8 PMG: relative residual = 5.392727e-06 PMG: contraction number = 4.055022e-01 NEWTON: using errtol_s: 4.024962e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.995170e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.256344e+01 PMG: contraction number = , 2.256344e+01 PMG: iteration = 9 PMG: relative residual = 2.720905e-06 PMG: contraction number = 5.045509e-01 NEWTON: using errtol_s: 2.030798e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.085860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.010484e+01 PMG: contraction number = , 1.010484e+01 PMG: iteration = 10 PMG: relative residual = 1.218482e-06 PMG: contraction number = 4.478221e-01 NEWTON: using errtol_s: 9.094363e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.176800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.073928e+00 PMG: contraction number = , 5.073928e+00 PMG: iteration = 11 PMG: relative residual = 6.118413e-07 PMG: contraction number = 5.021342e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.068890e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.108300e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 106.287) 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 = 2.511141092323E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.348771855344E+05 kT Vpmg_energy: dielEnergy = 1.674356589669E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.613000e+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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, 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 = 9.307000e+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 = 6.170000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.699000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.494040e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.409218e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.560360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.704806e+06 PMG: contraction number = , 3.704806e+06 NEWTON: attempting damping, relres = 2.459243e+03 NEWTON: attempting damping, relres = 5.712755e-01 NEWTON: attempting damping, relres = 7.734044e-01 NEWTON: damping accepted, relres = 5.712755e-01 PMG: iteration = 1 PMG: relative residual = 5.712755e-01 PMG: contraction number = 5.712755e-01 NEWTON: using errtol_s: 1.947603e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.708880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.076731e+06 PMG: contraction number = , 2.076731e+06 NEWTON: attempting damping, relres = 6.252154e-02 NEWTON: attempting damping, relres = 3.135534e-01 NEWTON: damping accepted, relres = 6.252154e-02 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 6.252154e-02 PMG: contraction number = 1.094420e-01 NEWTON: using errtol_s: 2.131496e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.827680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.886248e+05 PMG: contraction number = , 2.886248e+05 PMG: iteration = 3 PMG: relative residual = 9.587773e-03 PMG: contraction number = 1.533515e-01 NEWTON: using errtol_s: 3.268681e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.920360e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.192809e+04 PMG: contraction number = , 5.192809e+04 PMG: iteration = 4 PMG: relative residual = 1.954010e-03 PMG: contraction number = 2.038023e-01 NEWTON: using errtol_s: 6.661648e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.013480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.169499e+04 PMG: contraction number = , 1.169499e+04 PMG: iteration = 5 PMG: relative residual = 4.698460e-04 PMG: contraction number = 2.404522e-01 NEWTON: using errtol_s: 1.601807e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.106760e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.498917e+03 PMG: contraction number = , 3.498917e+03 PMG: iteration = 6 PMG: relative residual = 1.264642e-04 PMG: contraction number = 2.691610e-01 NEWTON: using errtol_s: 4.311441e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.199810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.222279e+03 PMG: contraction number = , 1.222279e+03 PMG: iteration = 7 PMG: relative residual = 3.645114e-05 PMG: contraction number = 2.882329e-01 NEWTON: using errtol_s: 1.242699e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.293580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.212491e+02 PMG: contraction number = , 4.212491e+02 PMG: iteration = 8 PMG: relative residual = 1.137574e-05 PMG: contraction number = 3.120818e-01 NEWTON: using errtol_s: 3.878238e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.387400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.392924e+02 PMG: contraction number = , 1.392924e+02 PMG: iteration = 9 PMG: relative residual = 3.690934e-06 PMG: contraction number = 3.244566e-01 NEWTON: using errtol_s: 1.258320e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.480420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.596052e+01 PMG: contraction number = , 4.596052e+01 PMG: iteration = 10 PMG: relative residual = 1.214340e-06 PMG: contraction number = 3.290063e-01 NEWTON: using errtol_s: 4.139951e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.573970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.472482e+01 PMG: contraction number = , 1.472482e+01 PMG: iteration = 11 PMG: relative residual = 3.887941e-07 PMG: contraction number = 3.201690e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.143230e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.182730e+03 Vpmg_setPart: lower corner = (-139.528, -166.004, -109.407) Vpmg_setPart: upper corner = (143.952, 160.29, 163.013) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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 = 7.826284585884E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 7.727509478979E+05 kT Vpmg_energy: dielEnergy = 3.862276160250E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.760000e+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 = 449 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 61, nyc = 65, nzc = 57 Vpmg_ctor2: PMG chose nf = 110792097, nc = 226005 Vpmg_ctor2: PMG chose narr = 126717744, narrc = 15925647 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1571140097, 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, 106.287 VPMG::focusFillBound -- Old mesh mins = -139.528, -166.004, -109.407 VPMG::focusFillBound -- Old mesh maxs = 143.952, 160.29, 163.013 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-139.528, -166.004, -109.407) Vpmg_setPart: actual maxima = (143.952, 160.29, 163.013) 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, 106.287) VPMG::extEnergy Old lower corner = (-139.528, -166.004, -109.407) VPMG::extEnergy Old upper corner = (143.952, 160.29, 163.013) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0195785 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0222913 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 = 1.360100e+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 = 6.150000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.697000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.844140e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.703036e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.916400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.585661e+06 PMG: contraction number = , 6.585661e+06 NEWTON: attempting damping, relres = 1.615823e+04 NEWTON: attempting damping, relres = 6.215362e-01 NEWTON: attempting damping, relres = 7.904915e-01 NEWTON: damping accepted, relres = 6.215362e-01 PMG: iteration = 1 PMG: relative residual = 6.215362e-01 PMG: contraction number = 6.215362e-01 NEWTON: using errtol_s: 2.301571e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.108200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.785379e+06 PMG: contraction number = , 3.785379e+06 NEWTON: attempting damping, relres = 1.060072e-01 NEWTON: attempting damping, relres = 3.602845e-01 NEWTON: damping accepted, relres = 1.060072e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.060072e-01 PMG: contraction number = 1.705567e-01 NEWTON: using errtol_s: 3.925484e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.217420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.554096e+05 PMG: contraction number = , 5.554096e+05 PMG: iteration = 3 PMG: relative residual = 1.789385e-02 PMG: contraction number = 1.687985e-01 NEWTON: using errtol_s: 6.626159e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.296970e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.024924e+05 PMG: contraction number = , 1.024924e+05 PMG: iteration = 4 PMG: relative residual = 3.967760e-03 PMG: contraction number = 2.217387e-01 NEWTON: using errtol_s: 1.469276e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.377230e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.865621e+04 PMG: contraction number = , 2.865621e+04 PMG: iteration = 5 PMG: relative residual = 1.176212e-03 PMG: contraction number = 2.964424e-01 NEWTON: using errtol_s: 4.355556e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.457440e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.019364e+04 PMG: contraction number = , 1.019364e+04 PMG: iteration = 6 PMG: relative residual = 3.903495e-04 PMG: contraction number = 3.318700e-01 NEWTON: using errtol_s: 1.445479e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.537720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.990821e+03 PMG: contraction number = , 3.990821e+03 PMG: iteration = 7 PMG: relative residual = 1.315814e-04 PMG: contraction number = 3.370862e-01 NEWTON: using errtol_s: 4.872508e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.617990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.487407e+03 PMG: contraction number = , 1.487407e+03 PMG: iteration = 8 PMG: relative residual = 4.061020e-05 PMG: contraction number = 3.086317e-01 NEWTON: using errtol_s: 1.503811e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.698240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.262113e+02 PMG: contraction number = , 5.262113e+02 PMG: iteration = 9 PMG: relative residual = 1.293743e-05 PMG: contraction number = 3.185758e-01 NEWTON: using errtol_s: 4.790776e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.778420e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.931125e+02 PMG: contraction number = , 1.931125e+02 PMG: iteration = 10 PMG: relative residual = 4.697637e-06 PMG: contraction number = 3.631045e-01 NEWTON: using errtol_s: 1.739552e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.857800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.329447e+01 PMG: contraction number = , 9.329447e+01 PMG: iteration = 11 PMG: relative residual = 2.267557e-06 PMG: contraction number = 4.827015e-01 NEWTON: using errtol_s: 8.396845e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.938080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.654290e+01 PMG: contraction number = , 5.654290e+01 PMG: iteration = 12 PMG: relative residual = 1.374243e-06 PMG: contraction number = 6.060457e-01 NEWTON: using errtol_s: 5.088872e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.017140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.488067e+01 PMG: contraction number = , 2.488067e+01 PMG: iteration = 13 PMG: relative residual = 6.047096e-07 PMG: contraction number = 4.400311e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.224770e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.263800e+03 Vpmg_setPart: lower corner = (-79.484, -93.1155, -52.681) Vpmg_setPart: upper corner = (83.908, 87.4015, 106.287) Vpmg_setPart: actual minima = (-79.484, -93.1155, -52.681) Vpmg_setPart: actual maxima = (83.908, 87.4015, 106.287) 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 = 7.779122642580E+01 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.848585530340E+06 kT Vpmg_energy: dielEnergy = 9.241472979053E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.471000e+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 = 8.183180e+03