############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Nov 27 16:37:47 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Nov 27 16:38:07 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_allh42.821.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb42.821.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, 89.108) Valist_getStatistics: Min atom coordinate: (-50.619, -58.189, -30.276) Valist_getStatistics: Molecule center: (0.424, 0.12, 29.416) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 89.108) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 33.054) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 61.081) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Nov 27 16:39:29 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_allh42.821.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb42.821.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, 89.108) Valist_getStatistics: Min atom coordinate: (-50.619, -58.189, -30.276) Valist_getStatistics: Molecule center: (0.424, 0.12, 29.416) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 89.108) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 33.054) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 61.081) 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 29.416 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.621792 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.352883 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.567527 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 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 178.646 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.814 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 114.108 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 83.429 114.108 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 29.416 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.621792 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.352883 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.567527 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 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 178.646 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.814 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 114.108 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 83.429 114.108 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 29.416 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = 0.424 0.12 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.569676, 0.607385, 0.621792 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.339478, 0.347121, 0.352883 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.595913, 0.5715, 0.567527 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 29.416 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 128.031 145.893 178.646 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -127.183 -145.653 -119.814 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 76.467 83.429 114.108 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 83.429 114.108 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 = 82.6224 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 122.064 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, 133.712) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 11834953 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 = 7.132000e+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 = 6.390000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.667000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104000e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.987380e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.684400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.539493e+06 PMG: contraction number = , 4.539493e+06 NEWTON: attempting damping, relres = 1.206244e+06 NEWTON: attempting damping, relres = 1.816422e+00 NEWTON: attempting damping, relres = 7.818447e-01 NEWTON: attempting damping, relres = 8.875000e-01 NEWTON: damping accepted, relres = 7.818447e-01 PMG: iteration = 1 PMG: relative residual = 7.818447e-01 PMG: contraction number = 7.818447e-01 NEWTON: using errtol_s: 3.117512e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.205200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.524655e+06 PMG: contraction number = , 3.524655e+06 NEWTON: attempting damping, relres = 1.735159e-01 NEWTON: attempting damping, relres = 4.364332e-01 NEWTON: damping accepted, relres = 1.735159e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.735159e-01 PMG: contraction number = 2.219314e-01 NEWTON: using errtol_s: 6.918737e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.199300e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.327834e+05 PMG: contraction number = , 7.327834e+05 PMG: iteration = 3 PMG: relative residual = 4.311431e-02 PMG: contraction number = 2.484747e-01 NEWTON: using errtol_s: 1.719131e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.922000e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.023823e+05 PMG: contraction number = , 2.023823e+05 PMG: iteration = 4 PMG: relative residual = 1.166566e-02 PMG: contraction number = 2.705751e-01 NEWTON: using errtol_s: 4.651541e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.644700e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.409680e+04 PMG: contraction number = , 6.409680e+04 PMG: iteration = 5 PMG: relative residual = 3.142163e-03 PMG: contraction number = 2.693515e-01 NEWTON: using errtol_s: 1.252900e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.365800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.136108e+04 PMG: contraction number = , 2.136108e+04 PMG: iteration = 6 PMG: relative residual = 8.418787e-04 PMG: contraction number = 2.679297e-01 NEWTON: using errtol_s: 3.356890e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.086900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.145094e+03 PMG: contraction number = , 7.145094e+03 PMG: iteration = 7 PMG: relative residual = 2.246638e-04 PMG: contraction number = 2.668600e-01 NEWTON: using errtol_s: 8.958200e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.808100e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.312142e+03 PMG: contraction number = , 2.312142e+03 PMG: iteration = 8 PMG: relative residual = 5.930955e-05 PMG: contraction number = 2.639925e-01 NEWTON: using errtol_s: 2.364897e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.579600e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.947701e+02 PMG: contraction number = , 6.947701e+02 PMG: iteration = 9 PMG: relative residual = 1.602786e-05 PMG: contraction number = 2.702409e-01 NEWTON: using errtol_s: 6.390918e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.299800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.975890e+02 PMG: contraction number = , 1.975890e+02 PMG: iteration = 10 PMG: relative residual = 4.466219e-06 PMG: contraction number = 2.786534e-01 NEWTON: using errtol_s: 1.780851e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002070e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.688173e+01 PMG: contraction number = , 5.688173e+01 PMG: iteration = 11 PMG: relative residual = 1.283921e-06 PMG: contraction number = 2.874739e-01 NEWTON: using errtol_s: 5.119483e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.551283e+01 PMG: contraction number = , 2.551283e+01 PMG: iteration = 12 PMG: relative residual = 5.758561e-07 PMG: contraction number = 4.485135e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.014860e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.052810e+03 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.814) Vpmg_setPart: upper corner = (128.031, 145.893, 178.646) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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 = 1.910168242975E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.304307499040E+05 kT Vpmg_energy: dielEnergy = 4.648128206955E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.463000e+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 = 82.6224 Vpbe_ctor2: solute dimensions = 105.196 x 119.298 x 122.064 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, 133.712) Vclist_setupGrid: Grid lower corner = (-57.7829, -65.3529, -37.4399) Vclist_assignAtoms: Have 11834953 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, 114.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.814 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 178.646 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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, 114.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.814) VPMG::extEnergy Old upper corner = (128.031, 145.893, 178.646) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.040167 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0465877 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 = 1.329300e+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 = 5.640000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.548000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.320790e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.319044e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.766325e+06 PMG: contraction number = , 7.766325e+06 NEWTON: attempting damping, relres = 2.015316e+06 NEWTON: attempting damping, relres = 1.572676e+00 NEWTON: attempting damping, relres = 7.970674e-01 NEWTON: attempting damping, relres = 8.956447e-01 NEWTON: damping accepted, relres = 7.970674e-01 PMG: iteration = 1 PMG: relative residual = 7.970674e-01 PMG: contraction number = 7.970674e-01 NEWTON: using errtol_s: 3.442569e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.540980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.082683e+06 PMG: contraction number = , 6.082683e+06 NEWTON: attempting damping, relres = 2.140654e-01 NEWTON: attempting damping, relres = 4.687623e-01 NEWTON: damping accepted, relres = 2.140654e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 2.140654e-01 PMG: contraction number = 2.685662e-01 NEWTON: using errtol_s: 9.245578e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.641750e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.055895e+06 PMG: contraction number = , 1.055895e+06 PMG: iteration = 3 PMG: relative residual = 4.629199e-02 PMG: contraction number = 2.162516e-01 NEWTON: using errtol_s: 1.999371e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.715220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.051702e+05 PMG: contraction number = , 3.051702e+05 PMG: iteration = 4 PMG: relative residual = 1.258774e-02 PMG: contraction number = 2.719205e-01 NEWTON: using errtol_s: 5.436701e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.788730e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.836788e+04 PMG: contraction number = , 8.836788e+04 PMG: iteration = 5 PMG: relative residual = 3.324403e-03 PMG: contraction number = 2.640984e-01 NEWTON: using errtol_s: 1.435824e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.862320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.864559e+04 PMG: contraction number = , 2.864559e+04 PMG: iteration = 6 PMG: relative residual = 9.211186e-04 PMG: contraction number = 2.770779e-01 NEWTON: using errtol_s: 3.978352e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.939400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.555352e+03 PMG: contraction number = , 9.555352e+03 PMG: iteration = 7 PMG: relative residual = 2.582334e-04 PMG: contraction number = 2.803476e-01 NEWTON: using errtol_s: 1.115322e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.022640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.242441e+03 PMG: contraction number = , 3.242441e+03 PMG: iteration = 8 PMG: relative residual = 7.466420e-05 PMG: contraction number = 2.891345e-01 NEWTON: using errtol_s: 3.224780e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.096220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.111602e+03 PMG: contraction number = , 1.111602e+03 PMG: iteration = 9 PMG: relative residual = 2.359965e-05 PMG: contraction number = 3.160772e-01 NEWTON: using errtol_s: 1.019279e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.169810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.269741e+02 PMG: contraction number = , 4.269741e+02 PMG: iteration = 10 PMG: relative residual = 8.907894e-06 PMG: contraction number = 3.774588e-01 NEWTON: using errtol_s: 3.847359e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.243330e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.916501e+02 PMG: contraction number = , 1.916501e+02 PMG: iteration = 11 PMG: relative residual = 3.994460e-06 PMG: contraction number = 4.484180e-01 NEWTON: using errtol_s: 1.725225e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.316850e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.827858e+01 PMG: contraction number = , 9.827858e+01 PMG: iteration = 12 PMG: relative residual = 2.048214e-06 PMG: contraction number = 5.127637e-01 NEWTON: using errtol_s: 8.846327e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.390370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.362114e+01 PMG: contraction number = , 5.362114e+01 PMG: iteration = 13 PMG: relative residual = 1.117461e-06 PMG: contraction number = 5.455783e-01 NEWTON: using errtol_s: 4.826364e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.463950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.014294e+01 PMG: contraction number = , 3.014294e+01 PMG: iteration = 14 PMG: relative residual = 6.281574e-07 PMG: contraction number = 5.621290e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.190520e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.226760e+03 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 114.108) 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 = 1.906818152267E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.179275358764E+06 kT Vpmg_energy: dielEnergy = 1.089235189431E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.351000e+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, 25.8901) 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 = 4.088000e+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 = 2.539000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.708560e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.877163e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.765890e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.893396e+05 PMG: contraction number = , 6.893396e+05 NEWTON: attempting damping, relres = 9.106477e-02 NEWTON: attempting damping, relres = 5.429469e-01 NEWTON: damping accepted, relres = 9.106477e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.106477e-02 PMG: contraction number = 9.106477e-02 NEWTON: using errtol_s: 6.262673e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.865090e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.183920e+04 PMG: contraction number = , 9.183920e+04 PMG: iteration = 2 PMG: relative residual = 1.202579e-02 PMG: contraction number = 1.320575e-01 NEWTON: using errtol_s: 8.270329e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.937400e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.473721e+04 PMG: contraction number = , 1.473721e+04 PMG: iteration = 3 PMG: relative residual = 1.928681e-03 PMG: contraction number = 1.603788e-01 NEWTON: using errtol_s: 1.326386e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.034410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.658869e+03 PMG: contraction number = , 2.658869e+03 PMG: iteration = 4 PMG: relative residual = 3.479620e-04 PMG: contraction number = 1.804145e-01 NEWTON: using errtol_s: 2.392992e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.106490e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.162014e+02 PMG: contraction number = , 5.162014e+02 PMG: iteration = 5 PMG: relative residual = 6.755491e-05 PMG: contraction number = 1.941445e-01 NEWTON: using errtol_s: 4.645861e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.178540e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.225195e+02 PMG: contraction number = , 1.225195e+02 PMG: iteration = 6 PMG: relative residual = 1.603389e-05 PMG: contraction number = 2.373461e-01 NEWTON: using errtol_s: 1.102677e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.250600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.837729e+01 PMG: contraction number = , 3.837729e+01 PMG: iteration = 7 PMG: relative residual = 5.022419e-06 PMG: contraction number = 3.132377e-01 NEWTON: using errtol_s: 3.454000e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.322650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.528747e+01 PMG: contraction number = , 1.528747e+01 PMG: iteration = 8 PMG: relative residual = 2.000640e-06 PMG: contraction number = 3.983418e-01 NEWTON: using errtol_s: 1.375873e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.394680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.615828e+00 PMG: contraction number = , 6.615828e+00 PMG: iteration = 9 PMG: relative residual = 8.658049e-07 PMG: contraction number = 4.327640e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.321000e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.675400e+02 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.814) Vpmg_setPart: upper corner = (128.031, 145.893, 178.646) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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 = 2.581603761527E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.381338790745E+05 kT Vpmg_energy: dielEnergy = 6.906390647039E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.422000e+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, 25.8901) 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, 114.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.814 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 178.646 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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, 114.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.814) VPMG::extEnergy Old upper corner = (128.031, 145.893, 178.646) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000170304 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000241552 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 = 6.870000e+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 = 5.630000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.536000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.570820e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465715e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.628160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.335987e+06 PMG: contraction number = , 1.335987e+06 NEWTON: attempting damping, relres = 1.618662e-01 NEWTON: attempting damping, relres = 5.803732e-01 NEWTON: damping accepted, relres = 1.618662e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.618662e-01 PMG: contraction number = 1.618662e-01 NEWTON: using errtol_s: 1.208447e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.727570e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.724139e+05 PMG: contraction number = , 1.724139e+05 PMG: iteration = 2 PMG: relative residual = 2.079210e-02 PMG: contraction number = 1.284523e-01 NEWTON: using errtol_s: 1.552279e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.799740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.546879e+04 PMG: contraction number = , 2.546879e+04 PMG: iteration = 3 PMG: relative residual = 3.070318e-03 PMG: contraction number = 1.476675e-01 NEWTON: using errtol_s: 2.292212e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.871900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.148459e+03 PMG: contraction number = , 4.148459e+03 PMG: iteration = 4 PMG: relative residual = 5.001025e-04 PMG: contraction number = 1.628830e-01 NEWTON: using errtol_s: 3.733623e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.944080e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.240359e+02 PMG: contraction number = , 7.240359e+02 PMG: iteration = 5 PMG: relative residual = 8.728396e-05 PMG: contraction number = 1.745321e-01 NEWTON: using errtol_s: 6.516372e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.016270e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.832748e+02 PMG: contraction number = , 1.832748e+02 PMG: iteration = 6 PMG: relative residual = 2.209403e-05 PMG: contraction number = 2.531282e-01 NEWTON: using errtol_s: 1.649477e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.088460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.094964e+01 PMG: contraction number = , 9.094964e+01 PMG: iteration = 7 PMG: relative residual = 1.096474e-05 PMG: contraction number = 4.962762e-01 NEWTON: using errtol_s: 8.185963e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.160600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.845751e+01 PMG: contraction number = , 3.845751e+01 PMG: iteration = 8 PMG: relative residual = 4.636107e-06 PMG: contraction number = 4.228196e-01 NEWTON: using errtol_s: 3.461185e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.232740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.773091e+01 PMG: contraction number = , 1.773091e+01 PMG: iteration = 9 PMG: relative residual = 2.137568e-06 PMG: contraction number = 4.610695e-01 NEWTON: using errtol_s: 1.595847e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.304870e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.975486e+00 PMG: contraction number = , 7.975486e+00 PMG: iteration = 10 PMG: relative residual = 9.614542e-07 PMG: contraction number = 4.497889e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.827200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.181900e+02 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 114.108) 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 = 2.508704670161E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.377745881820E+05 kT Vpmg_energy: dielEnergy = 1.688843626662E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.557000e+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 = 6.592000e+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 = 5.620000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.538000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.581370e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.299624e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.638710e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.853553e+06 PMG: contraction number = , 3.853553e+06 NEWTON: attempting damping, relres = 1.303796e+06 NEWTON: attempting damping, relres = 2.042276e+00 NEWTON: attempting damping, relres = 7.838867e-01 NEWTON: attempting damping, relres = 8.878992e-01 NEWTON: damping accepted, relres = 7.838867e-01 PMG: iteration = 1 PMG: relative residual = 7.838867e-01 PMG: contraction number = 7.838867e-01 NEWTON: using errtol_s: 2.586532e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.794040e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.987015e+06 PMG: contraction number = , 2.987015e+06 NEWTON: attempting damping, relres = 1.985820e-01 NEWTON: attempting damping, relres = 4.401318e-01 NEWTON: damping accepted, relres = 1.985820e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 1.985820e-01 PMG: contraction number = 2.533300e-01 NEWTON: using errtol_s: 6.552461e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.925640e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.676799e+05 PMG: contraction number = , 6.676799e+05 PMG: iteration = 3 PMG: relative residual = 5.154046e-02 PMG: contraction number = 2.595424e-01 NEWTON: using errtol_s: 1.700642e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.020240e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.943886e+05 PMG: contraction number = , 1.943886e+05 PMG: iteration = 4 PMG: relative residual = 1.426371e-02 PMG: contraction number = 2.767478e-01 NEWTON: using errtol_s: 4.706488e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.092460e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.357147e+04 PMG: contraction number = , 6.357147e+04 PMG: iteration = 5 PMG: relative residual = 3.890146e-03 PMG: contraction number = 2.727303e-01 NEWTON: using errtol_s: 1.283602e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.164610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.158229e+04 PMG: contraction number = , 2.158229e+04 PMG: iteration = 6 PMG: relative residual = 1.050324e-03 PMG: contraction number = 2.699960e-01 NEWTON: using errtol_s: 3.465674e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.236680e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.277502e+03 PMG: contraction number = , 7.277502e+03 PMG: iteration = 7 PMG: relative residual = 2.812598e-04 PMG: contraction number = 2.677839e-01 NEWTON: using errtol_s: 9.280518e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.308740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.364291e+03 PMG: contraction number = , 2.364291e+03 PMG: iteration = 8 PMG: relative residual = 7.419523e-05 PMG: contraction number = 2.637960e-01 NEWTON: using errtol_s: 2.448164e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.380830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.109775e+02 PMG: contraction number = , 7.109775e+02 PMG: iteration = 9 PMG: relative residual = 1.989382e-05 PMG: contraction number = 2.681280e-01 NEWTON: using errtol_s: 6.564212e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.452910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.007557e+02 PMG: contraction number = , 2.007557e+02 PMG: iteration = 10 PMG: relative residual = 5.485346e-06 PMG: contraction number = 2.757312e-01 NEWTON: using errtol_s: 1.809958e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.524960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.557710e+01 PMG: contraction number = , 5.557710e+01 PMG: iteration = 11 PMG: relative residual = 1.515969e-06 PMG: contraction number = 2.763670e-01 NEWTON: using errtol_s: 5.002127e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.597000e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.282893e+01 PMG: contraction number = , 2.282893e+01 PMG: iteration = 12 PMG: relative residual = 6.226787e-07 PMG: contraction number = 4.107465e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.061590e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.097070e+03 Vpmg_setPart: lower corner = (-127.183, -145.653, -119.814) Vpmg_setPart: upper corner = (128.031, 145.893, 178.646) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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 = 1.883217625499E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 7.922984023720E+05 kT Vpmg_energy: dielEnergy = 3.957498215884E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.392000e+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, 114.108 VPMG::focusFillBound -- Old mesh mins = -127.183, -145.653, -119.814 VPMG::focusFillBound -- Old mesh maxs = 128.031, 145.893, 178.646 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-127.183, -145.653, -119.814) Vpmg_setPart: actual maxima = (128.031, 145.893, 178.646) 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, 114.108) VPMG::extEnergy Old lower corner = (-127.183, -145.653, -119.814) VPMG::extEnergy Old upper corner = (128.031, 145.893, 178.646) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.0399453 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.0462859 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 = 1.141400e+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 = 5.600000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.536000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.818160e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.572469e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.875580e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.433127e+06 PMG: contraction number = , 6.433127e+06 NEWTON: attempting damping, relres = 2.265177e+06 NEWTON: attempting damping, relres = 1.752537e+00 NEWTON: attempting damping, relres = 7.983777e-01 NEWTON: attempting damping, relres = 8.957669e-01 NEWTON: damping accepted, relres = 7.983777e-01 PMG: iteration = 1 PMG: relative residual = 7.983777e-01 PMG: contraction number = 7.983777e-01 NEWTON: using errtol_s: 2.852180e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.026430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.039263e+06 PMG: contraction number = , 5.039263e+06 NEWTON: attempting damping, relres = 2.353870e-01 NEWTON: attempting damping, relres = 4.711286e-01 NEWTON: damping accepted, relres = 2.353870e-01 NEWTON: damping disabled... PMG: iteration = 2 PMG: relative residual = 2.353870e-01 PMG: contraction number = 2.948317e-01 NEWTON: using errtol_s: 8.409130e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.132150e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.277942e+05 PMG: contraction number = , 9.277942e+05 PMG: iteration = 3 PMG: relative residual = 5.369343e-02 PMG: contraction number = 2.281070e-01 NEWTON: using errtol_s: 1.918181e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.226180e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.880677e+05 PMG: contraction number = , 2.880677e+05 PMG: iteration = 4 PMG: relative residual = 1.508964e-02 PMG: contraction number = 2.810333e-01 NEWTON: using errtol_s: 5.390729e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.297910e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.641364e+04 PMG: contraction number = , 8.641364e+04 PMG: iteration = 5 PMG: relative residual = 4.053998e-03 PMG: contraction number = 2.686609e-01 NEWTON: using errtol_s: 1.448278e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.369620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.838880e+04 PMG: contraction number = , 2.838880e+04 PMG: iteration = 6 PMG: relative residual = 1.128090e-03 PMG: contraction number = 2.782660e-01 NEWTON: using errtol_s: 4.030066e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.446630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.532193e+03 PMG: contraction number = , 9.532193e+03 PMG: iteration = 7 PMG: relative residual = 3.162950e-04 PMG: contraction number = 2.803811e-01 NEWTON: using errtol_s: 1.129954e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.540630e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.226935e+03 PMG: contraction number = , 3.226935e+03 PMG: iteration = 8 PMG: relative residual = 9.067471e-05 PMG: contraction number = 2.866777e-01 NEWTON: using errtol_s: 3.239326e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.612320e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.094439e+03 PMG: contraction number = , 1.094439e+03 PMG: iteration = 9 PMG: relative residual = 2.817430e-05 PMG: contraction number = 3.107183e-01 NEWTON: using errtol_s: 1.006518e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.683980e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.124770e+02 PMG: contraction number = , 4.124770e+02 PMG: iteration = 10 PMG: relative residual = 1.040672e-05 PMG: contraction number = 3.693695e-01 NEWTON: using errtol_s: 3.717770e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.755600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.823588e+02 PMG: contraction number = , 1.823588e+02 PMG: iteration = 11 PMG: relative residual = 4.595156e-06 PMG: contraction number = 4.415565e-01 NEWTON: using errtol_s: 1.641606e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.827200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.329465e+01 PMG: contraction number = , 9.329465e+01 PMG: iteration = 12 PMG: relative residual = 2.350682e-06 PMG: contraction number = 5.115565e-01 NEWTON: using errtol_s: 8.397740e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.898830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.103053e+01 PMG: contraction number = , 5.103053e+01 PMG: iteration = 13 PMG: relative residual = 1.285720e-06 PMG: contraction number = 5.469560e-01 NEWTON: using errtol_s: 4.593194e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970430e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.882973e+01 PMG: contraction number = , 2.882973e+01 PMG: iteration = 14 PMG: relative residual = 7.263447e-07 PMG: contraction number = 5.649324e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 1.197950e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.233380e+03 Vpmg_setPart: lower corner = (-75.619, -83.189, -55.276) Vpmg_setPart: upper corner = (76.467, 83.429, 114.108) Vpmg_setPart: actual minima = (-75.619, -83.189, -55.276) Vpmg_setPart: actual maxima = (76.467, 83.429, 114.108) 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 = 1.880353098681E+02 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.841502256381E+06 kT Vpmg_energy: dielEnergy = 9.203517414679E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.338000e+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 = 7.126540e+03