Hi,<br>
<br>
Just another addition to the earlier statements... The distance from
the peptide to the wall should be at least min(0.5*cut-off, 1 nm). If
the cut-off is smaller than 2 nm (and in general people use around 1.5
nm), then you still want to have a distance of at least 1 nm to the
wall to get bulk-like behaviour as Oliver stated. <br>
<br>
Also, if the peptide is flexible, then you need to have a shell of
water which will fit the extended conformation, in order not to allow
direct interactions between periodic images. The best choice of box in
such a case is the rhombic dodecahedron...<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 11/2/05, <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;">
Mikko Hellgren wrote:<br><br>>Hi,
I have a general question about MD simulations in GROMACS and that is
how thick water layer that one should add around a peptide. Is there
some general rules to this. I imagine that this should depend on size
and the stability of the peptide in a water solution?<br>><br>><br>The basic rule is related to the cutoff !!! You want to make sure that<br>one molecule<br>will not see another molecule and its image. That would be introduce
<br>periodicity in<br>your system ... no good. That is sepecially true for the solvent !!!<br><br>Ideal: size of the box > 2*cutoff. which can be seen as distance from<br>the protein to<br>the edge > cutoff.<br><br>
Best<br>XAvier<br><br>--<br>----------------------------------<br> Xavier Periole - Ph.D.<br><br> Dept. of Biophysical Chemistry / MD Group<br> Univ. of Groningen<br> Nijenborgh 4<br> 9747 AG Groningen<br> The Netherlands
<br><br> Tel: +31-503634329<br> Fax: +31-503634800<br> email: <a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br> web-page: <a href="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</a><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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