[gmx-users] How thick layer of water should one add around a protein?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 2 11:50:31 CET 2005


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.

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...



On 11/2/05, Xavier Periole <x.periole at rug.nl> wrote:
> Mikko Hellgren wrote:
> >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?
> >
> >
> The basic rule is related to the cutoff !!! You want to make sure that
> one molecule
> will not see another molecule and its image. That would be introduce
> periodicity in
> your system ... no good. That is sepecially true for the solvent !!!
> Ideal: size of the box > 2*cutoff. which can be seen as distance from
> the protein to
> the edge > cutoff.
> Best
> XAvier
> --
> ----------------------------------
> Xavier Periole - Ph.D.
> Dept. of Biophysical Chemistry / MD Group
> Univ. of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Tel: +31-503634329
> Fax: +31-503634800
> email: x.periole at rug.nl
> web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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