I have encountered the same problem too. For water molecules not being broken in the mdrun, I think atoms in same charge group will not be divided into separate processors. It will be ok to use trjconv -pbc nojump/mol to get a clear visualization.
> > Hi Justin, > > It's indeed the case that mdrun now writes broken molecules. Has to do > with the domain decomposition and processors only keeping track of > 'their' atoms. Too bad, but you'll just have to keep a .tpr around to > make molecules whole again afterwards. Using trjconv -nojump with a > suitable reference (not necessarily a .tpr) would also do it (and > simultaneously remove the jumps...). > > Cheers, > > Tsjerk > > On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > Hi, > > > > I've been running some simulations with Gromacs 4.0 RC2, and I've noticed > > something strange. In the output .gro file at the end of a run, the > > molecules in my system (a membrane protein) are broken, crossing periodic > > boundaries. This affects the lipids at the periphery of the box, in my > case. > > > > Has there been some change since the previous version that mdrun is now > > writing broken molecules to fit everything within the unit cell? Or is > this > > behavior unintentional? > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > _______________________________________________ > > 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 [EMAIL PROTECTED] > > 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 > >
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