Dept. Biotechnology Ext. 3108
----- Forwarded Message ----- From: "Ms. Aswathy S" <[email protected]> To: [email protected] Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Segmentation fault while running gromacs 4.0.4 Hi, I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation. But when I run the grommp for equilibration of about 30 ps, it shows Segmentaion Fault. I din't get any idea that what type of error it causing from the log file. When i run the free command it has a free space of 33 MB. Is that could be the reason?. But I already read that gromacs doesnot consume that much memory(10-20Mb). If so tell me what could be the possibilities. attaching the mdp file and log file I will explain all the steps i have did, 1. The protein and ligand i minimized in vaccum. 2. Then added water and again minimized the whole system (During both 1 & 2 minimization, "Steepest Descents converged to machine precision "in early steps ) 3. I used the otput file from the above result for equilibration steps(is that the reason??!!!) then i faced the segmentatuion fault. Please help me.... thanks in advance.... Dept. Biotechnology Ext. 3108
Log file opened on Mon Jun 1 11:53:59 2009 Host: localhost.localdomain pid: 8316 nodeid: 0 nnodes: 1 The Gromacs distribution was built Wed May 13 12:15:31 IST 2009 by [email protected] (Linux 2.6.18-92.el5xen i686) :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ 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 = 5000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode = Linear nstlog = 100 nstxout = 250 nstvout = 1000 nstfout = 0 nstenergy = 10 nstxtcout = 100 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 60 nky = 60 nkz = 60 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Berendsen epc = Berendsen epctype = Isotropic tau_p = 0.5 ref_p (3x3): ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} compress (3x3): compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} refcoord_scaling = No posres_com (3): posres_com[0]= 0.00000e+00 posres_com[1]= 0.00000e+00 posres_com[2]= 0.00000e+00 posres_comB (3): posres_comB[0]= 0.00000e+00 posres_comB[1]= 0.00000e+00 posres_comB[2]= 0.00000e+00 andersen_seed = 815131 rlist = 1 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = No free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 nwall = 0 wall_type = 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre = No 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 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs 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: 5507.76 63693.2 ref_t: 310 310 tau_t: 0.1 0.1 anneal: No No ann_npoints: 0 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 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE 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 --- -------- -------- Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 0.000 Generated table with 1000 data points for Ewald. Tabscale = 500 points/nm Generated table with 1000 data points for LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for LJ12. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC water optimization for 10603 molecules. Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Removing pbc first time ++++ 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 --- -------- -------- Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ 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 --- -------- -------- There are: 33671 Atoms Max number of connections per atom is 30 Total number of connections is 69215 Max number of graph edges per atom is 4 Total number of graph edges is 46198 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 1.76638e-06 K Started mdrun on node 0 Mon Jun 1 11:54:00 2009 Step Time Lambda 0 0.00000 0.00000 Grid: 11 x 11 x 11 cells Large VCM(group rest): -1848358.87500, 8457395.00000, 2829469.25000, Temp-cm: 3.18509e+15 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 4.97530e+05 2.07949e+03 9.36503e+02 3.85386e+01 2.48016e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80823e+04 1.57962e+05 7.88847e+18 -6.03984e+04 7.88847e+18 Kinetic En. Total Energy Temperature Pressure (bar) 3.40354e+37 3.40354e+37 inf 1.08894e+36
md.mdp
Description: Binary data
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