Log file opened: nodeid 0, nnodes = 1, host = unknown, process = 2388 :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 3.1.2 (-: 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 = steep nsteps = 700 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstenergy = 100 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 104 nky = 104 nkz = 104 pme_order = 4 ewald_rtol = 0 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bUncStart = FALSE bShakeSOR = FALSE etc = No epc = No epctype = Isotropic tau_p = 1 ref_p (3x3): ref_p[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000} ref_p[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000} ref_p[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000} compress (3x3): compress[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000} compress[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000} compress[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000} bSimAnn = FALSE zero_temp_time = 0 rlist = 0.9 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 vdwtype = Cut-off rvdw_switch = 0 rvdw = 0.9 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 = 1000 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 ConstAlg = Lincs shake_tol = 0.0001 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: 545976 ref_t: 0 tau_t: 0 acc: 0 0 0 nfreeze: N N N energygrp_excl[ 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=64234, targetcg=32117, myshift= 0 nsb->shift = 1, nsb->bshift= 0 Neighbor Search Blocks nsb->nodeid: 0 nsb->nnodes: 1 nsb->cgtotal: 64235 nsb->natoms: 181993 nsb->shift: 1 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 181993 64235 64235 Max number of bonds per atom is 4 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0 nm for Ewald Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9 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 Generated table with 750 data points for Ewald. Tabscale = 500 points/nm Generated table with 750 data points for LJ6. Tabscale = 500 points/nm Generated table with 750 data points for LJ12. Tabscale = 500 points/nm Going to determine what solvent types we have. There are 56295 molecules, 64235 charge groups and 181993 atoms There are 0 optimized solvent molecules on node 0 There are 56293 optimized water molecules on node 0 Will do PME sum in reciprocal space. ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen {A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using the FFTW library (Fastest Fourier Transform in the West) Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 1.16138e+006 Started Steepest Descents on node 0 Thu Oct 30 14:11:02 2003 Removing pbc first time Done rmpbc Steepest Descents: Tolerance = 1.00000e+003 Number of steps = 700 Grid: 27 x 27 x 27 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 0.00000 Step Time Lambda Annealing 1 1.00000 0.00000 0.00000 Step Time Lambda Annealing 2 2.00000 0.00000 0.00000 Step Time Lambda Annealing 3 3.00000 0.00000 0.00000 Step Time Lambda Annealing 4 4.00000 0.00000 0.00000 Step Time Lambda Annealing 5 5.00000 0.00000 0.00000 Step Time Lambda Annealing 6 6.00000 0.00000 0.00000 Step Time Lambda Annealing 7 7.00000 0.00000 0.00000 Step Time Lambda Annealing 8 8.00000 0.00000 0.00000 Step Time Lambda Annealing 9 9.00000 0.00000 0.00000 Step Time Lambda Annealing 10 10.00000 0.00000 0.00000 Step Time Lambda Annealing 11 11.00000 0.00000 0.00000 Step Time Lambda Annealing 12 12.00000 0.00000 0.00000 Step Time Lambda Annealing 13 13.00000 0.00000 0.00000 Step Time Lambda Annealing 14 14.00000 0.00000 0.00000 Stepsize too small (6.10352e-007 nm)Converged to machine precision, but not to the requested precision (1000) Steepest Descents did not converge in 15 steps Potential Energy = -1.#IND0e+000 Maximum force: 4.13872e+006 M E G A - F L O P S A C C O U N T I N G RF=Reaction-field Free=Free Energy SC=Softcore T=Tabulated S=Solvent W=Water WW=Water-Water Computing: M-Number M-Flop's % Flop's LJ 1.865069 57.817139 0.6 LJ + Coulomb 0.359400 13.657200 0.1 Coulomb(T) 0.409124 16.774084 0.2 Coulomb(T)(W) 0.030774 3.785202 0.0 LJ + Coulomb(T) 0.462895 24.996330 0.2 LJ + Coulomb(T)(W) 0.083496 11.355456 0.1 LJ + Coulomb(T)(WW) 2.733193 1019.480989 10.0 Innerloop-Iatom 0.810235 8.102350 0.1 Spread Q Bspline 174.713280 349.426560 3.4 Gather F Bspline 174.713280 2096.559360 20.6 3D-FFT 678.337500 5426.700000 53.2 Solve PME 8.436480 539.934720 5.3 NS-Pairs 11.883494 249.553374 2.4 Reset In Box 2.729895 24.569055 0.2 Shift-X 2.729895 16.379370 0.2 CG-CoM 0.963525 27.942225 0.3 Bonds 1.888905 81.222915 0.8 Angles 1.135215 185.040045 1.8 Propers 0.108105 24.756045 0.2 Impropers 0.098940 20.579520 0.2 Virial 0.000405 0.007290 0.0 Total 10198.63923 100.0 NODE (s) Real (s) (%) Time: 25607.000 25607.000 100.0 7h06:47 Finished mdrun on node 0 Thu Oct 30 21:17:49 2003