############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Nov 27 19:04:12 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_dmpg_allh41.821.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb41.821.pdb NOsh: Storing molecule 2 path dmpg.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 = (449, 481, 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 = (449, 481, 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 = (449, 481, 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 33171 atoms Valist_getStatistics: Max atom coordinate: (51.467, 58.429, 88.108) Valist_getStatistics: Min atom coordinate: (-50.619, -58.189, -30.276) Valist_getStatistics: Molecule center: (0.424, 0.12, 28.916) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 88.108) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 32.054) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 60.081) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Nov 27 19:04:37 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_dmpg_allh41.821.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb41.821.pdb NOsh: Storing molecule 2 path dmpg.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 = (449, 481, 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 = (449, 481, 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 = (449, 481, 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 33171 atoms Valist_getStatistics: Max atom coordinate: (51.467, 58.429, 88.108) Valist_getStatistics: Min atom coordinate: (-50.619, -58.189, -30.276) Valist_getStatistics: Molecule center: (0.424, 0.12, 28.916) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 88.108) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 32.054) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 60.081) Valist_readPDB: Counted 28416 atoms Valist_getStatistics: Max atom coordinate: (51.467, 58.429, 29.054) Valist_getStatistics: Min atom coordinate: (-50.619, -58.189, -30.276) Valist_getStatistics: Molecule center: (0.424, 0.12, -0.611) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.616583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.3508 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.568942 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 176.896 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.064 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.619 -83.189 -55.276 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.619 -83.189 -55.276 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.616583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.3508 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.568942 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 176.896 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.064 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.619 -83.189 -55.276 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.619 -83.189 -55.276 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.616583 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.3508 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.568942 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = 0.424 0.12 28.916 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 176.896 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.064 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.619 -83.189 -55.276 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 76.467 83.429 113.108 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.619 -83.189 -55.276 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 = 82.3704 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 121.064 Vpbe_ctor2: solute charge = -262.15 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 = (116.414, 130.946, 132.712) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 11899900 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 7.131000e+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 = 5.580000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.552000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079800e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.991316e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.672900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.548070e+06 PMG: contraction number = , 4.548070e+06 NEWTON: attempting damping, relres = 1.083536e+06 NEWTON: attempting damping, relres = 1.791308e+00 NEWTON: attempting damping, relres = 7.819075e-01 NEWTON: attempting damping, relres = 8.875217e-01 NEWTON: damping accepted, relres = 7.819075e-01 PMG: iteration = 1 PMG: relative residual = 7.819075e-01 PMG: contraction number = 7.819075e-01 NEWTON: using errtol_s: 3.120840e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.194000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.532595e+06 PMG: contraction number = , 3.532595e+06 NEWTON: attempting damping, relres = 1.733765e-01 NEWTON: attempting damping, relres = 4.364704e-01 NEWTON: damping accepted, relres = 1.733765e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.733765e-01 PMG: contraction number = 2.217353e-01 NEWTON: using errtol_s: 6.920002e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.189900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.302602e+05 PMG: contraction number = , 7.302602e+05 PMG: iteration = 3 PMG: relative residual = 4.297410e-02 PMG: contraction number = 2.478658e-01 NEWTON: using errtol_s: 1.715232e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.913900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.005391e+05 PMG: contraction number = , 2.005391e+05 PMG: iteration = 4 PMG: relative residual = 1.160659e-02 PMG: contraction number = 2.700834e-01 NEWTON: using errtol_s: 4.632556e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.637900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.322121e+04 PMG: contraction number = , 6.322121e+04 PMG: iteration = 5 PMG: relative residual = 3.129791e-03 PMG: contraction number = 2.696564e-01 NEWTON: using errtol_s: 1.249199e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.361000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.113175e+04 PMG: contraction number = , 2.113175e+04 PMG: iteration = 6 PMG: relative residual = 8.423473e-04 PMG: contraction number = 2.691385e-01 NEWTON: using errtol_s: 3.362074e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.136000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.236014e+03 PMG: contraction number = , 7.236014e+03 PMG: iteration = 7 PMG: relative residual = 2.287087e-04 PMG: contraction number = 2.715135e-01 NEWTON: using errtol_s: 9.128486e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.081700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.510888e+03 PMG: contraction number = , 2.510888e+03 PMG: iteration = 8 PMG: relative residual = 6.510552e-05 PMG: contraction number = 2.846657e-01 NEWTON: using errtol_s: 2.598567e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.804400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.960831e+02 PMG: contraction number = , 8.960831e+02 PMG: iteration = 9 PMG: relative residual = 2.094690e-05 PMG: contraction number = 3.217377e-01 NEWTON: using errtol_s: 8.360569e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.526300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.288539e+02 PMG: contraction number = , 3.288539e+02 PMG: iteration = 10 PMG: relative residual = 7.455671e-06 PMG: contraction number = 3.559320e-01 NEWTON: using errtol_s: 2.975794e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.201404e+02 PMG: contraction number = , 1.201404e+02 PMG: iteration = 11 PMG: relative residual = 2.711615e-06 PMG: contraction number = 3.636983e-01 NEWTON: using errtol_s: 1.082291e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.197169e+01 PMG: contraction number = , 4.197169e+01 PMG: iteration = 12 PMG: relative residual = 9.466244e-07 PMG: contraction number = 3.490998e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.034930e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.070490e+03 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.064) Vpmg_setPart: upper corner = (128.031, 145.893, 176.896) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = 1.910947248992E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.351623387842E+05 kT Vpmg_energy: dielEnergy = 4.671785481089E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.387000e+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 = 82.3704 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 121.064 Vpbe_ctor2: solute charge = -262.15 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 = (116.414, 130.946, 132.712) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 11899900 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.619, -83.189, -55.276 VPMG::focusFillBound -- New mesh maxs = 76.467, 83.429, 113.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.064 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 176.896 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = (-75.619, -83.189, -55.276) VPMG::extEnergy Disj part upper corner = (76.467, 83.429, 113.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.064) VPMG::extEnergy Old upper corner = (128.031, 145.893, 176.896) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0379823 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0440518 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 = 1.238700e+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 = 5.590000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.551000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.328000e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.319234e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.773808e+06 PMG: contraction number = , 7.773808e+06 NEWTON: attempting damping, relres = 3.494412e+06 NEWTON: attempting damping, relres = 1.611997e+00 NEWTON: attempting damping, relres = 7.971618e-01 NEWTON: attempting damping, relres = 8.956692e-01 NEWTON: damping accepted, relres = 7.971618e-01 PMG: iteration = 1 PMG: relative residual = 7.971618e-01 PMG: contraction number = 7.971618e-01 NEWTON: using errtol_s: 3.443128e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.538260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.088143e+06 PMG: contraction number = , 6.088143e+06 NEWTON: attempting damping, relres = 2.121054e-01 NEWTON: attempting damping, relres = 4.687999e-01 NEWTON: damping accepted, relres = 2.121054e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 2.121054e-01 PMG: contraction number = 2.660757e-01 NEWTON: using errtol_s: 9.161329e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.637080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.053307e+06 PMG: contraction number = , 1.053307e+06 PMG: iteration = 3 PMG: relative residual = 4.551890e-02 PMG: contraction number = 2.146051e-01 NEWTON: using errtol_s: 1.966067e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.708960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.010702e+05 PMG: contraction number = , 3.010702e+05 PMG: iteration = 4 PMG: relative residual = 1.227091e-02 PMG: contraction number = 2.695783e-01 NEWTON: using errtol_s: 5.300091e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.584028e+04 PMG: contraction number = , 8.584028e+04 PMG: iteration = 5 PMG: relative residual = 3.196018e-03 PMG: contraction number = 2.604550e-01 NEWTON: using errtol_s: 1.380435e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.852650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.717583e+04 PMG: contraction number = , 2.717583e+04 PMG: iteration = 6 PMG: relative residual = 8.684639e-04 PMG: contraction number = 2.717331e-01 NEWTON: using errtol_s: 3.751099e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.924500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.744000e+03 PMG: contraction number = , 8.744000e+03 PMG: iteration = 7 PMG: relative residual = 2.376604e-04 PMG: contraction number = 2.736561e-01 NEWTON: using errtol_s: 1.026511e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.996190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.799512e+03 PMG: contraction number = , 2.799512e+03 PMG: iteration = 8 PMG: relative residual = 6.499960e-05 PMG: contraction number = 2.734978e-01 NEWTON: using errtol_s: 2.807485e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.067950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.736244e+02 PMG: contraction number = , 8.736244e+02 PMG: iteration = 9 PMG: relative residual = 1.857332e-05 PMG: contraction number = 2.857452e-01 NEWTON: using errtol_s: 8.022253e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.139780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.993184e+02 PMG: contraction number = , 2.993184e+02 PMG: iteration = 10 PMG: relative residual = 6.246733e-06 PMG: contraction number = 3.363282e-01 NEWTON: using errtol_s: 2.698110e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.211580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.302490e+02 PMG: contraction number = , 1.302490e+02 PMG: iteration = 11 PMG: relative residual = 2.714043e-06 PMG: contraction number = 4.344739e-01 NEWTON: using errtol_s: 1.172259e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.283410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.747141e+01 PMG: contraction number = , 6.747141e+01 PMG: iteration = 12 PMG: relative residual = 1.405909e-06 PMG: contraction number = 5.180128e-01 NEWTON: using errtol_s: 6.072449e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.355190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.588004e+01 PMG: contraction number = , 3.588004e+01 PMG: iteration = 13 PMG: relative residual = 7.476349e-07 PMG: contraction number = 5.317805e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.072850e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.108400e+03 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 113.108) 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 = 1.907725522010E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.185369876096E+06 kT Vpmg_energy: dielEnergy = 1.092282046252E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.230000e+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, 24.8901) 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 4.076000e+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 = 5.590000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.549000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.581980e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.884364e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.641160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.933563e+05 PMG: contraction number = , 6.933563e+05 NEWTON: attempting damping, relres = 9.149637e-02 NEWTON: attempting damping, relres = 5.431772e-01 NEWTON: damping accepted, relres = 9.149637e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.149637e-02 PMG: contraction number = 9.149637e-02 NEWTON: using errtol_s: 6.298943e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.740380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.234457e+04 PMG: contraction number = , 9.234457e+04 PMG: iteration = 2 PMG: relative residual = 1.207912e-02 PMG: contraction number = 1.320174e-01 NEWTON: using errtol_s: 8.315702e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.812540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.478076e+04 PMG: contraction number = , 1.478076e+04 PMG: iteration = 3 PMG: relative residual = 1.932363e-03 PMG: contraction number = 1.599755e-01 NEWTON: using errtol_s: 1.330309e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.884640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.650221e+03 PMG: contraction number = , 2.650221e+03 PMG: iteration = 4 PMG: relative residual = 3.464675e-04 PMG: contraction number = 1.792973e-01 NEWTON: using errtol_s: 2.385208e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.956670e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.091689e+02 PMG: contraction number = , 5.091689e+02 PMG: iteration = 5 PMG: relative residual = 6.656495e-05 PMG: contraction number = 1.921247e-01 NEWTON: using errtol_s: 4.582574e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.028820e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.200081e+02 PMG: contraction number = , 1.200081e+02 PMG: iteration = 6 PMG: relative residual = 1.568881e-05 PMG: contraction number = 2.356917e-01 NEWTON: using errtol_s: 1.080075e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.100980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.037566e+01 PMG: contraction number = , 4.037566e+01 PMG: iteration = 7 PMG: relative residual = 5.278460e-06 PMG: contraction number = 3.364475e-01 NEWTON: using errtol_s: 3.633884e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.173020e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.822142e+01 PMG: contraction number = , 1.822142e+01 PMG: iteration = 8 PMG: relative residual = 2.382107e-06 PMG: contraction number = 4.512883e-01 NEWTON: using errtol_s: 1.639929e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.245040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.334610e+00 PMG: contraction number = , 8.334610e+00 PMG: iteration = 9 PMG: relative residual = 1.089605e-06 PMG: contraction number = 4.574123e-01 NEWTON: using errtol_s: 7.501238e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.317090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.546388e+00 PMG: contraction number = , 3.546388e+00 PMG: iteration = 10 PMG: relative residual = 4.636231e-07 PMG: contraction number = 4.254964e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.809800e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.165100e+02 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.064) Vpmg_setPart: upper corner = (128.031, 145.893, 176.896) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = 2.578734545027E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.388217340177E+05 kT Vpmg_energy: dielEnergy = 6.940783779698E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.417000e+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, 24.8901) 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.619, -83.189, -55.276 VPMG::focusFillBound -- New mesh maxs = 76.467, 83.429, 113.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.064 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 176.896 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = (-75.619, -83.189, -55.276) VPMG::extEnergy Disj part upper corner = (76.467, 83.429, 113.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.064) VPMG::extEnergy Old upper corner = (128.031, 145.893, 176.896) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0001548 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000218948 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 = 6.864000e+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 = 5.590000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.549000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.493090e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465825e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.552290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.333556e+06 PMG: contraction number = , 1.333556e+06 NEWTON: attempting damping, relres = 1.615647e-01 NEWTON: attempting damping, relres = 5.802372e-01 NEWTON: damping accepted, relres = 1.615647e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.615647e-01 PMG: contraction number = 1.615647e-01 NEWTON: using errtol_s: 1.206214e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.651700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.715897e+05 PMG: contraction number = , 1.715897e+05 PMG: iteration = 2 PMG: relative residual = 2.069247e-02 PMG: contraction number = 1.280754e-01 NEWTON: using errtol_s: 1.544864e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.723900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.532817e+04 PMG: contraction number = , 2.532817e+04 PMG: iteration = 3 PMG: relative residual = 3.053319e-03 PMG: contraction number = 1.475570e-01 NEWTON: using errtol_s: 2.279554e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.796120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.138140e+03 PMG: contraction number = , 4.138140e+03 PMG: iteration = 4 PMG: relative residual = 4.988508e-04 PMG: contraction number = 1.633798e-01 NEWTON: using errtol_s: 3.724332e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.868400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.058219e+02 PMG: contraction number = , 7.058219e+02 PMG: iteration = 5 PMG: relative residual = 8.508678e-05 PMG: contraction number = 1.705656e-01 NEWTON: using errtol_s: 6.352429e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.940690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.555116e+02 PMG: contraction number = , 1.555116e+02 PMG: iteration = 6 PMG: relative residual = 1.874684e-05 PMG: contraction number = 2.203261e-01 NEWTON: using errtol_s: 1.399606e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.012880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.451362e+01 PMG: contraction number = , 6.451362e+01 PMG: iteration = 7 PMG: relative residual = 7.777349e-06 PMG: contraction number = 4.148619e-01 NEWTON: using errtol_s: 5.806433e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.085180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.174895e+01 PMG: contraction number = , 3.174895e+01 PMG: iteration = 8 PMG: relative residual = 3.827320e-06 PMG: contraction number = 4.921111e-01 NEWTON: using errtol_s: 2.857410e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.157380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.335958e+01 PMG: contraction number = , 1.335958e+01 PMG: iteration = 9 PMG: relative residual = 1.610540e-06 PMG: contraction number = 4.208011e-01 NEWTON: using errtol_s: 1.202401e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.229560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.041813e+00 PMG: contraction number = , 6.041813e+00 PMG: iteration = 10 PMG: relative residual = 7.283368e-07 PMG: contraction number = 4.522313e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.824200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.179500e+02 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 113.108) 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 = 2.509223106260E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.386753770003E+05 kT Vpmg_energy: dielEnergy = 1.693347565375E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.398000e+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 = 75.3735 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 62.053 Vpbe_ctor2: solute charge = -256 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 = (116.414, 130.946, 73.6578) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 16007974 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, 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 = 6.596000e+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 = 5.570000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.551000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.485670e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.302953e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.544870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.858294e+06 PMG: contraction number = , 3.858294e+06 NEWTON: attempting damping, relres = 1.129511e+06 NEWTON: attempting damping, relres = 1.994170e+00 NEWTON: attempting damping, relres = 7.838614e-01 NEWTON: attempting damping, relres = 8.879081e-01 NEWTON: damping accepted, relres = 7.838614e-01 PMG: iteration = 1 PMG: relative residual = 7.838614e-01 PMG: contraction number = 7.838614e-01 NEWTON: using errtol_s: 2.589058e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.696910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.992121e+06 PMG: contraction number = , 2.992121e+06 NEWTON: attempting damping, relres = 1.988621e-01 NEWTON: attempting damping, relres = 4.401380e-01 NEWTON: damping accepted, relres = 1.988621e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.988621e-01 PMG: contraction number = 2.536955e-01 NEWTON: using errtol_s: 6.568323e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.796290e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.650463e+05 PMG: contraction number = , 6.650463e+05 PMG: iteration = 3 PMG: relative residual = 5.152305e-02 PMG: contraction number = 2.590894e-01 NEWTON: using errtol_s: 1.701782e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.868510e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.925473e+05 PMG: contraction number = , 1.925473e+05 PMG: iteration = 4 PMG: relative residual = 1.423207e-02 PMG: contraction number = 2.762272e-01 NEWTON: using errtol_s: 4.700785e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.940770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.281913e+04 PMG: contraction number = , 6.281913e+04 PMG: iteration = 5 PMG: relative residual = 3.886014e-03 PMG: contraction number = 2.730464e-01 NEWTON: using errtol_s: 1.283532e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.012920e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.139933e+04 PMG: contraction number = , 2.139933e+04 PMG: iteration = 6 PMG: relative residual = 1.053395e-03 PMG: contraction number = 2.710735e-01 NEWTON: using errtol_s: 3.479316e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.085040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.382966e+03 PMG: contraction number = , 7.382966e+03 PMG: iteration = 7 PMG: relative residual = 2.864763e-04 PMG: contraction number = 2.719552e-01 NEWTON: using errtol_s: 9.462179e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.157200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.568876e+03 PMG: contraction number = , 2.568876e+03 PMG: iteration = 8 PMG: relative residual = 8.138141e-05 PMG: contraction number = 2.840773e-01 NEWTON: using errtol_s: 2.687990e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.229410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.199939e+02 PMG: contraction number = , 9.199939e+02 PMG: iteration = 9 PMG: relative residual = 2.611083e-05 PMG: contraction number = 3.208452e-01 NEWTON: using errtol_s: 8.624287e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.301640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.389420e+02 PMG: contraction number = , 3.389420e+02 PMG: iteration = 10 PMG: relative residual = 9.294503e-06 PMG: contraction number = 3.559635e-01 NEWTON: using errtol_s: 3.069931e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.373860e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.243954e+02 PMG: contraction number = , 1.243954e+02 PMG: iteration = 11 PMG: relative residual = 3.393305e-06 PMG: contraction number = 3.650872e-01 NEWTON: using errtol_s: 1.120793e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.446040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.395231e+01 PMG: contraction number = , 4.395231e+01 PMG: iteration = 12 PMG: relative residual = 1.197940e-06 PMG: contraction number = 3.530306e-01 NEWTON: using errtol_s: 3.956741e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.518250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.423313e+01 PMG: contraction number = , 1.423313e+01 PMG: iteration = 13 PMG: relative residual = 3.878468e-07 PMG: contraction number = 3.237614e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.078510e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.114040e+03 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.064) Vpmg_setPart: upper corner = (128.031, 145.893, 176.896) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = 1.883110187167E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 7.963423205889E+05 kT Vpmg_energy: dielEnergy = 3.977718913690E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.395000e+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 = 75.3735 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 62.053 Vpbe_ctor2: solute charge = -256 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 = (116.414, 130.946, 73.6578) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 16007974 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 = 449, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 57, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 103881089, nc = 212097 Vpmg_ctor2: PMG chose narr = 118815844, narrc = 14934755 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1473243677, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.619, -83.189, -55.276 VPMG::focusFillBound -- New mesh maxs = 76.467, 83.429, 113.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.064 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 176.896 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.064) Vpmg_setPart: actual maxima = (128.031, 145.893, 176.896) 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 = (-75.619, -83.189, -55.276) VPMG::extEnergy Disj part upper corner = (76.467, 83.429, 113.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.064) VPMG::extEnergy Old upper corner = (128.031, 145.893, 176.896) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0378277 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0438075 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 = 1.145000e+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 = 5.590000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.549000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.739910e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.572650e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.799200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.443039e+06 PMG: contraction number = , 6.443039e+06 NEWTON: attempting damping, relres = 3.756844e+06 NEWTON: attempting damping, relres = 1.780901e+00 NEWTON: attempting damping, relres = 7.984424e-01 NEWTON: attempting damping, relres = 8.957989e-01 NEWTON: damping accepted, relres = 7.984424e-01 PMG: iteration = 1 PMG: relative residual = 7.984424e-01 PMG: contraction number = 7.984424e-01 NEWTON: using errtol_s: 2.852555e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.950250e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.048204e+06 PMG: contraction number = , 5.048204e+06 NEWTON: attempting damping, relres = 2.336249e-01 NEWTON: attempting damping, relres = 4.712406e-01 NEWTON: damping accepted, relres = 2.336249e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 2.336249e-01 PMG: contraction number = 2.926008e-01 NEWTON: using errtol_s: 8.346601e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.049120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.280512e+05 PMG: contraction number = , 9.280512e+05 PMG: iteration = 3 PMG: relative residual = 5.298500e-02 PMG: contraction number = 2.267951e-01 NEWTON: using errtol_s: 1.892969e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.120890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.858180e+05 PMG: contraction number = , 2.858180e+05 PMG: iteration = 4 PMG: relative residual = 1.479040e-02 PMG: contraction number = 2.791431e-01 NEWTON: using errtol_s: 5.284091e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.192690e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.437157e+04 PMG: contraction number = , 8.437157e+04 PMG: iteration = 5 PMG: relative residual = 3.917430e-03 PMG: contraction number = 2.648631e-01 NEWTON: using errtol_s: 1.399561e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.264490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.709494e+04 PMG: contraction number = , 2.709494e+04 PMG: iteration = 6 PMG: relative residual = 1.068424e-03 PMG: contraction number = 2.727361e-01 NEWTON: using errtol_s: 3.817107e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.336260e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.776796e+03 PMG: contraction number = , 8.776796e+03 PMG: iteration = 7 PMG: relative residual = 2.926898e-04 PMG: contraction number = 2.739452e-01 NEWTON: using errtol_s: 1.045678e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.408060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.801702e+03 PMG: contraction number = , 2.801702e+03 PMG: iteration = 8 PMG: relative residual = 7.948463e-05 PMG: contraction number = 2.715662e-01 NEWTON: using errtol_s: 2.839708e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.479800e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.644784e+02 PMG: contraction number = , 8.644784e+02 PMG: iteration = 9 PMG: relative residual = 2.229601e-05 PMG: contraction number = 2.805071e-01 NEWTON: using errtol_s: 7.965583e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.551570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.852535e+02 PMG: contraction number = , 2.852535e+02 PMG: iteration = 10 PMG: relative residual = 7.200451e-06 PMG: contraction number = 3.229480e-01 NEWTON: using errtol_s: 2.572469e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.623340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.199346e+02 PMG: contraction number = , 1.199346e+02 PMG: iteration = 11 PMG: relative residual = 3.021379e-06 PMG: contraction number = 4.196096e-01 NEWTON: using errtol_s: 1.079433e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.695130e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.078618e+01 PMG: contraction number = , 6.078618e+01 PMG: iteration = 12 PMG: relative residual = 1.531294e-06 PMG: contraction number = 5.068198e-01 NEWTON: using errtol_s: 5.470780e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.766940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.286277e+01 PMG: contraction number = , 3.286277e+01 PMG: iteration = 13 PMG: relative residual = 8.278601e-07 PMG: contraction number = 5.406276e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.072740e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.108310e+03 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 113.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 113.108) 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 = 1.880408814838E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.846696144494E+06 kT Vpmg_energy: dielEnergy = 9.229484434205E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.256000e+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. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.918250e+03