Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham<mark.abra...@anu.edu.au> wrote: > Jamie Seyed wrote: >> >> Dear all, >> I performed an md simulation but it crashed at the beginning because >> according to it "system was exploding". Also when I tried to see the >> system >> by ngmx, there was no water anymore and it was only the molecule sitting >> in >> the box(after grompp and before mdrun it was a box of water plus the >> molecule)!!?? > > So you used a wrong file at some point... name your files carefully, and use > them carefully.
Maybe xtc-grps was set to "protein"? That wouldn't be related to the problem. But did the crash occur directly, at step -1/0/1, or did the system run at least for a few steps? What exactly were you doing? Please copy-paste your command lines, your .mdp file and the mdrun output (not the log file yet, please). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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
