Hi,<br>
<br>
Just to add my 5 cEUR. The flying ice cube will be avoided using linear
comm removal on the whole system (default), which will retain diffusion
of the peptide in the solvent. The peaks you see in the comm I guess
are due to the update of the neighbour list (every ten steps?). This
will change the system a bit more than usually, causing the peptide to
suddenly see different interacting particles.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 12/26/07, <b class="gmail_sendername">Xavier Periole</b> <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</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, 26 Dec 2007 09:01:22 +0100<br> David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>> Li Qiang wrote:<br>>> hi Christian,<br>>><br>>> Thanks for the reply. I have plotted the the rate of center of mass
<br>>> motion and found there are peaks with certain time interval. I think<br>>> that is not only a visual problem but like fly ice cube problem(not<br>>> sure). As a comparison, when a large protein is simulated, the
<br>>> rate(velocity) of COM is "constant".<br>>><br><br>I do not think you want to remove the center of mass motion of your<br>peptide, and certainly not of your solvent. The diffusion of the peptide
<br>is certainly something you should expect. If it looks like a flying<br>ice cube that means that there are some parameters that you should<br>modify in your mdp file.<br><br>>> Yes. the default way GROMACS do is system COM removal at each step.
<br>>><br>>><br>>> how does the program remove this center of mass motion?<br>>><br>> By summing the COM momentum and subtracting it from all atoms.<br>><br>> --<br>> David van der Spoel,
Ph.D.<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<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://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>> _______________________________________________<br>> gmx-users mailing list
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<br>XAvier Periole - PhD<br><br>NMR & Molecular Dynamics Group<br>University of Groningen<br>The Netherlands<br><a href="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</a><br>-----------------------------------------------------
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</div><br><br clear="all"><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
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