Hi Emma,<br><br>When using -pbc whole you should provide a run input (.tpr) file. But under normal circumstances your molecules wouldn't be broken in an original .trr file. You could try to run trjconv without any particular option: trjconv -f
input.trr -o output.gro -s reference.tpr<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 11/17/05, <b class="gmail_sendername">Viswanadham Sridhara</b> <<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">What about the initial structure of the run?<div><span class="e" id="q_107a01097f3aac4c_1">
<br><br><div><span class="gmail_quote">On 11/17/05, <b class="gmail_sendername">Emma Falck</b> <<a href="mailto:efalck@cc.hut.fi" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">efalck@cc.hut.fi</a>
> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>My problem is with the trjconv command. I am trying to convert a trajectory<br>in the .trr format to a trajectory in the .gro format, such that the<br>molecules are whole in the resulting trajectory. To do so, I use trjconv
<br>with the option '-pbc whole'. Even so, my molecules -- both lipids and<br>water molecules -- are broken in the resulting .gro file.<br><br>I recently installed Gromacs 3.3 to my PowerBook, that runs OS X 10.4.<br>I did not compile Gromacs from the source, but used the OS X package provided
<br>on the gromacs pages.<br><br>Has anyone else had related/similar problems with trjconv, in particular with<br>OS X?<br><br>Best regards,<br><br>Emma<br><br>--<br>Dr. Emma Falck<br>Beckman Institute, UIUC<br>_______________________________________________
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<br></span></div><span class="sg">-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>
Old Dominion University, "VIRGINIA".<br>
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gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>