Log file opened: nodeid 0, nnodes = 1, host = shspc8.chem.psu.edu, process = 7441 :-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- There are 0 atoms for free energy perturbation Input Parameters: integrator = md nsteps = 2000 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 nstlog = 10 nstxout = 100 nstvout = 100 nstfout = 100 nstenergy = 10 nstxtcout = 0 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bUncStart = FALSE bShakeSOR = FALSE etc = No epc = No epctype = Isotropic tau_p = 0.5 ref_p (3x3): ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} bSimAnn = FALSE zero_temp_time = 0 rlist = 0.9 coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 1.4 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.4 epsilon_r = 1 DispCorr = No fudgeQQ = 1 free_energy = no init_lambda = 0 sc_alpha = 0 sc_sigma = 0.3 delta_lambda = 0 disre_weighting = Conservative disre_mixed = FALSE dr_fc = 1000 dr_tau = 0 nstdisreout = 100 orires_fc = 0 orires_tau = 0 nstorireout = 100 em_stepsize = 0.01 em_tol = 100 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 ConstAlg = Lincs shake_tol = 1e-04 lincs_order = 4 lincs_warnangle = 30 bd_temp = 300 bd_fric = 0 ld_seed = 1993 cos_accel = 0 userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 10670.6 63789.5 2465.9 ref_t: 0 0 0 tau_t: 0 0 0 acc: 0 0 0 nfreeze: Y Y Y N N N energygrp_excl[ 0]: 0 0 0 energygrp_excl[ 1]: 0 0 0 energygrp_excl[ 2]: 0 0 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 CPU= 0, lastcg= 9483, targetcg= 4742, myshift= 0 nsb->shift = 1, nsb->bshift= 0 Neighbor Search Blocks nsb->nodeid: 0 nsb->nnodes: 1 nsb->cgtotal: 9484 nsb->natoms: 25693 nsb->shift: 1 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 25693 9484 9484 Max number of bonds per atom is 4 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.9 Coulomb: 1.4 LJ: 1.4 Generated table with 500 data points for COUL. Tabscale = 500 points/nm Generated table with 500 data points for LJ6. Tabscale = 500 points/nm Generated table with 500 data points for LJ12. Tabscale = 500 points/nm Going to determine what solvent types we have. There are 7365 molecules, 9484 charge groups and 25693 atoms There are 0 optimized solvent molecules on node 0 There are 7362 optimized water molecules on node 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 173087 There are: 25693 Atom Removing pbc first time Done rmpbc Started mdrun on node 0 Mon Sep 20 10:24:34 2004 Initial temperature: 100.196 K Grid: 8 x 9 x 9 cells Testing x86 processor CPUID... Testing x86 SSE capabilities... CPU and OS support SSE. Using Gromacs SSE single precision assembly innerloops. Step Time Lambda Annealing 0 0.00000 0.00000 1.00000 Large VCM(group rest): 38.68133, -25.79747, 4.84125, ekin-cm: 189114400.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.83121e+08 1.95949e+05 1.72870e+03 5.27783e+04 2.03325e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) 3.50973e+04 7.78084e+06 3.18191e+14 -3.64129e+05 -2.12314e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) 3.18191e+14 5.02768e+26 5.02768e+26 1.57213e+24 2.03218e+25 Large VCM(group rest): -68.41705, 164.31322, 743.00323, ekin-cm: 50518392832.00000 Large VCM(group rest): 13.91927, -36.10575, -897.67261, ekin-cm: 69867806720.00000 Large VCM(group rest): -248.72539, 565.04205, 1092.14514, ekin-cm: 136212496384.00000 Large VCM(group rest): 7978.58252, 15956.94922, -12725.16309, ekin-cm: 41559248601088.00000 Fatal error: ci = -2147483648 should be in 0 .. 647 [FILE nsgrid.c, LINE 210]