Hi Maggin, Okay, this image may require a bit of explanation :p VMD has drawn bonds according to the bondedness in a reference file. But the atoms have moved, and some went over the box boundaries. So they show up with long bonds crossing the whole box. It's not a problem, just a visualization artefact.
Cheers, Tsjerk On Mon, Jun 17, 2013 at 7:52 AM, maggin <maggin.c...@gmail.com> wrote: > Hi, all > > When I run a small peptide at NVT stage, I get a snapshot like this: > > <http://gromacs.5086.x6.nabble.com/file/n5009206/next6_gro2.bmp> > > I am not sure if it right, and can I use it for NPT ? > > Thank you very much! > > maggin > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists