<br>
Hi Xie Yinghong,<br>
<br>
When simulating under periodic boundary conditions, mdrun constantly
chooses the best copy of each molecule for reference, giving rise to
jumps over the boundaries. When you have a number of large molecules,
the COM of these together may jump quite a bit, if one of the proteins
jumps. It is better to select one group consisting of small parts, such
as the solvent or a lipid bilayer, or one of the larger molecules in
your system for VCM removal to avoid jumps in the COM.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<br><div><span class="gmail_quote">On 10/12/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
On Wed, 2005-10-12 at 12:10 -0800, Yinghong wrote:<br><br>> Because in my system, several protein chains are included. So, Did I<br>> need to make C.O.M removal for every seperated group? For example, is<br>> it ok for me to define "comm_grps = Protein1 Protein2 Protein3"?
<br>><br>You only want to do this in very special cases like<br>membrane/protein/water systems. Here you want just one group.<br><br><br>><br>><br>> Thanks in advance.<br>><br>><br>><br>><br>><br>
> Xie Yinghong<br>><br>> Hong Kong Univ.<br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>
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<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
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