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<div>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.</div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br>Hi Justin,<br><br>It's indeed the case that mdrun now writes broken molecules. Has to do<br>
with the domain decomposition and processors only keeping track of<br>'their' atoms. Too bad, but you'll just have to keep a .tpr around to<br>make molecules whole again afterwards. Using trjconv -nojump with a<br>
suitable reference (not necessarily a .tpr) would also do it (and<br>simultaneously remove the jumps...).<br><br>Cheers,<br><br>Tsjerk<br><br>On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>> Hi,<br>><br>> I've been running some simulations with Gromacs 4.0 RC2, and I've noticed<br>> something strange. In the output .gro file at the end of a run, the<br>> molecules in my system (a membrane protein) are broken, crossing periodic<br>
> boundaries. This affects the lipids at the periphery of the box, in my case.<br>><br>> Has there been some change since the previous version that mdrun is now<br>> writing broken molecules to fit everything within the unit cell? Or is this<br>
> behavior unintentional?<br>><br>> -Justin<br>><br>> --<br>> ========================================<br>><br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>
> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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><br><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>
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