I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.<br><br><div><span class="gmail_quote">On 4/24/06, <b class="gmail_sendername">Martin LEPSIK
</b> <<a href="mailto:martin.lepsik@ibs.fr">martin.lepsik@ibs.fr</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;">Dear GROMACS users,
<br><br>I would like to ask you maybe a trivial question: What is the best way<br>to image a protein with a ligand inside<br>a triclinic water box?<br><br>I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and "comm_mode" not
<br>set. I watch the movie in VMD,<br>loading first a starting gro and than the trr. The problem is that the<br>protein creeps out of the box (the same happens<br>when using ngmx).<br><br>I have tried various variants of post-processing using trjconv -fit
<br>(translation) -pbc (inbox, whole) -center (tric),<br>groups for fitting: protein or system. But in any case, the result is<br>the same.<br><br>Could you please advice me how to solve this? Whether it is better to<br>include some parameter for
<br>mdrun or to post-process in a different way?<br><br>Looking forward to hearing from you.<br><br>Yours sincerely,<br><br>Martin Lepsik<br><br>--<br>--------------------------<br>Martin Lepsik, Ph.D.<br>Laboratoire de Dynamique Moléculaire (LDM)
<br>Institut de Biologie Structurale<br>41, rue Jules Horowitz<br>38027 Grenoble Cedex 1, France<br>tel: +33-4-3878-4780<br>e-mail: <a href="mailto:martin.lepsik@ibs.fr">martin.lepsik@ibs.fr</a><br><br><br><br>_______________________________________________
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