############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:54:39 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:54:46 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_wATP_heptamer_1.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:55:13 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_wATP_heptamer_1.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:55:56 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:56:42 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_wATP_heptamer_1.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:59:08 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 15:59:38 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_wATP_heptamer_1.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:00:34 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:00:42 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_wATP_heptamer_1.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:27:43 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:27:54 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_noATP.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = 5, dime = (193, 193, 193) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:41:15 2011 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Jan 14 16:41:23 2011 ############################################################################## 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 /home/slars/gulrotkake/groel_md/1XCK/129_1XCK_MGATP/results/traj_heptamer/last_frame_noATP.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... 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 cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe 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 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 sdens... PBEparm_parseToken: trying sdens... 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 = (257, 129, 225) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 54845 atoms Valist_getStatistics: Max atom coordinate: (76.497, 122.415, 84.516) Valist_getStatistics: Min atom coordinate: (-71.199, 41.867, -59.027) Valist_getStatistics: Molecule center: (2.649, 82.141, 12.7445) NOsh_setupCalcMGAUTO(nosh.c, 1526): coarse grid center = 2.549 82.041 12.6815 NOsh_setupCalcMGAUTO(nosh.c, 1531): fine grid center = 2.549 82.041 12.6815 NOsh_setupCalcMGAUTO (nosh.c, 1543): Coarse grid spacing = 0.999387, 1.10697, 1.1112 NOsh_setupCalcMGAUTO (nosh.c, 1545): Fine grid spacing = 0.666, 0.807406, 0.742933 NOsh_setupCalcMGAUTO (nosh.c, 1547): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.666408, 0.729387, 0.668586 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1641): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1643): coarse mesh center = 2.549 82.041 12.6815 NOsh_setupCalcMGAUTO (nosh.c, 1648): coarse mesh upper corner = 130.471 152.887 137.136 NOsh_setupCalcMGAUTO (nosh.c, 1653): coarse mesh lower corner = -125.373 11.1952 -111.773 NOsh_setupCalcMGAUTO (nosh.c, 1658): initial fine mesh upper corner = 87.797 133.715 95.89 NOsh_setupCalcMGAUTO (nosh.c, 1663): initial fine mesh lower corner = -82.699 30.367 -70.527 NOsh_setupCalcMGAUTO (nosh.c, 1724): final fine mesh upper corner = 87.797 133.715 95.89 NOsh_setupCalcMGAUTO (nosh.c, 1729): final fine mesh lower corner = -82.699 30.367 -70.527 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 81.3959 Vpbe_ctor2: solute dimensions = 150.496 x 83.348 x 146.417 Vpbe_ctor2: solute charge = -125.963 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 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 2.5 max radius Vclist_setupGrid: Grid lengths = (159.908, 92.76, 155.755) Vclist_setupGrid: Grid lower corner = (-77.305, 35.761, -65.133) Vclist_assignAtoms: Have 14959332 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 257, ny = 129, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 33, nyc = 17, nzc = 29 Vpmg_ctor2: PMG chose nf = 7459425, nc = 16269 Vpmg_ctor2: PMG chose narr = 8545464, narrc = 1086039 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 97709117, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.182000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.280000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 8.090000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021100e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 6.072978e-02 PMG: contraction number = 6.072978e-02 PMG: iteration = 2 PMG: relative residual = 6.165942e-03 PMG: contraction number = 1.015308e-01 PMG: iteration = 3 PMG: relative residual = 1.091970e-03 PMG: contraction number = 1.770971e-01 PMG: iteration = 4 PMG: relative residual = 2.296747e-04 PMG: contraction number = 2.103305e-01 PMG: iteration = 5 PMG: relative residual = 6.093985e-05 PMG: contraction number = 2.653311e-01 PMG: iteration = 6 PMG: relative residual = 1.597179e-05 PMG: contraction number = 2.620911e-01 PMG: iteration = 7 PMG: relative residual = 4.719193e-06 PMG: contraction number = 2.954704e-01 PMG: iteration = 8 PMG: relative residual = 1.321073e-06 PMG: contraction number = 2.799363e-01 PMG: iteration = 9 PMG: relative residual = 4.046338e-07 PMG: contraction number = 3.062917e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 2.086000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.063000e+01 Vpmg_setPart: lower corner = (-125.373, 11.1952, -111.773) Vpmg_setPart: upper corner = (130.471, 152.887, 137.136) Vpmg_setPart: actual minima = (-125.373, 11.1952, -111.773) Vpmg_setPart: actual maxima = (130.471, 152.887, 137.136) 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).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 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 = 81.3959 Vpbe_ctor2: solute dimensions = 150.496 x 83.348 x 146.417 Vpbe_ctor2: solute charge = -125.963 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.125256 Vpbe_ctor2: Debye length = 7.98362 Vpbe_ctor2: zkappa2 = 1.22376 Vpbe_ctor2: zmagic = 6773.76 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 2.5 max radius Vclist_setupGrid: Grid lengths = (159.908, 92.76, 155.755) Vclist_setupGrid: Grid lower corner = (-77.305, 35.761, -65.133) Vclist_assignAtoms: Have 14959332 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 232.352 Vacc_storeParms: Using 2352-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 257, ny = 129, nz = 225 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 33, nyc = 17, nzc = 29 Vpmg_ctor2: PMG chose nf = 7459425, nc = 16269 Vpmg_ctor2: PMG chose narr = 8545464, narrc = 1086039 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 97709117, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -82.699, 30.367, -70.527 VPMG::focusFillBound -- New mesh maxs = 87.797, 133.715, 95.89 VPMG::focusFillBound -- Old mesh mins = -125.373, 11.1952, -111.773 VPMG::focusFillBound -- Old mesh maxs = 130.471, 152.887, 137.136 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 = 1.002000e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (MGDRIV2: fine pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro). CPU TIME = 1.290000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro).. Vnm_tstop: stopping timer 30 (MGDRIV2: coarse pro). CPU TIME = 7.980000e+00 Vnm_tstart: starting timer 30 (MGDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.329700e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 PMG: iteration = 1 PMG: relative residual = 9.229419e-02 PMG: contraction number = 9.229419e-02 PMG: iteration = 2 PMG: relative residual = 1.005080e-02 PMG: contraction number = 1.088996e-01 PMG: iteration = 3 PMG: relative residual = 1.677648e-03 PMG: contraction number = 1.669169e-01 PMG: iteration = 4 PMG: relative residual = 3.827293e-04 PMG: contraction number = 2.281345e-01 PMG: iteration = 5 PMG: relative residual = 1.284377e-04 PMG: contraction number = 3.355837e-01 PMG: iteration = 6 PMG: relative residual = 4.816009e-05 PMG: contraction number = 3.749684e-01 PMG: iteration = 7 PMG: relative residual = 2.103877e-05 PMG: contraction number = 4.368508e-01 PMG: iteration = 8 PMG: relative residual = 8.928395e-06 PMG: contraction number = 4.243781e-01 PMG: iteration = 9 PMG: relative residual = 4.005583e-06 PMG: contraction number = 4.486342e-01 PMG: iteration = 10 PMG: relative residual = 1.779356e-06 PMG: contraction number = 4.442189e-01 PMG: iteration = 11 PMG: relative residual = 7.903148e-07 PMG: contraction number = 4.441579e-01 Vnm_tstop: stopping timer 30 (MGDRIV2: solve). CPU TIME = 2.549000e+01 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.516000e+01 Vpmg_setPart: lower corner = (-82.699, 30.367, -70.527) Vpmg_setPart: upper corner = (87.797, 133.715, 95.89) Vpmg_setPart: actual minima = (-82.699, 30.367, -70.527) Vpmg_setPart: actual maxima = (87.797, 133.715, 95.89) 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).. Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 0.000000e+00 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_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.646300e+02