Dear gmx users, While running final md run some unexpected message is coming which i am not able to understand.. Pls help. I am attaching md.log file with this mail.
-- Sheetal Arora M.Tech(Biotechnology & Medical Engg) NIT Rourkela
Log file opened on Fri Apr 17 09:37:41 2009 Host: localhost1.localdomain pid: 3293 nodeid: 0 nnodes: 1 The Gromacs distribution was built Fri Mar 20 17:46:50 IST 2009 by [email protected] (Linux 2.6.18-53.el5PAE i686) :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. 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 READ AND 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 READ AND 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 --- -------- -------- Input Parameters: integrator = md nsteps = 500000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 comm_mode = Linear nstcheckpoint = 1000 nstlog = 5000 nstxout = 2500 nstvout = 5000 nstfout = 0 nstenergy = 500 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 88 nky = 88 nkz = 88 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bUncStart = FALSE bShakeSOR = FALSE etc = Berendsen 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} andersen_seed = 815131 rlist = 1.4 coulombtype = PME rcoulomb_switch = 0.8 rcoulomb = 1.4 vdwtype = Cut-off rvdw_switch = 0.8 rvdw = 1.4 epsilon_r = 1 epsilon_rf = 1 tabext = 1 gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No DispCorr = No fudgeQQ = 1 free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 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 dihre-fc = 1000 dihre-tau = 0 nstdihreout = 100 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Shake shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 lincs_iter = 1 bd_fric = 0 ld_seed = 1993 cos_accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 166617 ref_t: 298 tau_t: 0.1 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp_flags[ 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 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 CPU= 0, lastcg=29596, targetcg=14798, myshift= 0 nsb->shift = 1, nsb->bshift= 0 Neighbor Search Blocks nsb->nodeid: 0 nsb->nnodes: 1 nsb->cgtotal: 29597 nsb->natoms: 83355 nsb->shift: 1 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 83355 29597 29597 Max number of graph edges 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 0.448228 nm for Ewald Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4 System total charge: 0.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 500 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC water optimization for 25510 molecules. Will do PME sum in reciprocal space. ++++ PLEASE READ AND 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 --- -------- -------- Removing pbc first time Done rmpbc Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein, initial mass: 76290.6 1: SOL, initial mass: 459520 2: UNK, initial mass: 238.241 3: Na, initial mass: 505.776 4: Mg, initial mass: 24.305 There are: 83355 Atoms Constraining the starting coordinates (step -2) ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes J. Comp. Phys. 23 (1977) pp. 327-341 -------- -------- --- Thank You --- -------- --------
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