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

[Tsjerk Wassenaar]

Hi,

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...

Cheers,

Tsjerk

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
> ----------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



--

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051102/876f8574/attachment.html>