Re: RE : [gmx-users] segmentation fault in mdrun when using PME

[Arneh Babakhani]

Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference).  Also running Gromacs 3.3.1 Arneh title = ResMD warnings = 10 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50.0 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein sol ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: ________________________________ De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). Still doesn't work. logfile ends in the usual way. Except this time, I get this output: Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. ------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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