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

Xavier Periole x.periole at rug.nl
Wed Nov 2 11:27:59 CET 2005

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.


 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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