Right, there was no reference whatsoever to MD. The first sentence, preluding the problem, mentioned editconf. The second, mentioned trjconv. No grompp/mdrun etc in between. Anyway, also to check the periodicity in your output (note how flexibly I adapt it to the current situation):
genconf -f confout.gro -o out.pdb -nbox 2 2 2 :p Tsjerk On Sun, Jun 21, 2009 at 1:33 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote: > Omer Markovitch wrote: >> >> Thanks. >> I am not sure how this addresses my problem. I am getting "broken" >> structure at the end of the MD (in confout.gro), > > Well, you didn't say you were doing MD. I (and presumably Tsjerk) thought > you were converting your output from editconf. In such a case, Tserk's > suggestion lets you tile some boxes together to see how things are (not) > working. Your results will also depend on the contents of your editconf -f > file.gro. I suggest you copy and paste your actual commands in future :-) > > Mark > >> and want to be sure that GMX treat it correctly during the MD. >> >> To check your periodicity use genconf: >> >> genconf -f in.pdb -o out.pdb -nbox 2 2 2 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@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 > > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- 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
