Hi, do you get any other error messages? (Check md.log and the output)
You might want to use 4.0.4 instead of 4.0.2. (Some bugs have been fixed) Roland 2009/3/22 KS Rotondi <k...@chemistry.umass.edu>: > Dearest All, > > I'm experiencing strange behavior running Gromacs 4.0.2 on dual G5 > macintoshs (OS 10.4.11) in my college's computer laboratory. When I use the > attached .mdp file, grompp ends in a seg fault, however if I remove the last > 3 lines (controlling velocity generation) grompp runs normally and generates > a working .tpr file. In fact, simply changing gen_vel to no removes the > segmentation fault. To further complicate matters, this behavior is not seen > on my personal dual G5 running 10.5.4 (i.e. the attached .mdp file works > without modifications). > > Does anyone have any insight into this behavior? > > Thanks in advance, > > Ken > > include = -I../top > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 15000 ; total 30 ps. > nstxout = 5000 ; cord to .trr file every 10 ps. > nstvout = 5000 ; velo to .trr file every 10 ps. > nstfout = 5000 ; force to .trr file every 10 ps. > nstlog = 5000 ; energ to log file every 10ps. > nstenergy = 250 ; energ to energ file every 0.5ps > nstxtcout = 250 ; cood to .xtc file every 0.5ps > xtc_grps = Protein SOL > nstlist = 5 ; freq (steps) update neighbor list > ns_type = grid > pbc = xyz ; turns on periodic bound. cond. > rlist = 1.5 > coulombtype = PME > rcoulomb = 1.5 > vdwtype = switch > rvdw = 1.4 > rvdw_switch = 1.0 > ; Berendsen temperature coupling is on in two groups > tcoupl = Berendsen > tc_grps = Protein SOL > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Energy monitoring > energygrps = Protein SOL > ; Generate velocities is on at 300 K. > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > Dr. K.S. Rotondi > Departments of Chemistry, BIochemistry and Molecular Biology > 914G LGRT > The University of Massachusetts - Amherst > Amherst, MA 01003 > "If there's a solution, why worry?, If there's no solution, why worry?" > His Holiness, the Dalai Llama > > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
