Dear all, Thanks for all comments. I will check again all steps for my previous simulation with right files (according to Mark) and then I will let you know if I got the same problem (I am not working on proteins). Another question: --After energy minimization step for in-vacuo run, Should I do still position restrained MD, since I want the bond length be fixed (constraints=all-bonds)? --After pr-md in mdrun step for in-vacuo simulation, is it true that I will get the movement of my molecule in vacuum?? I appreciate your help/Jamie
On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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 >
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