tsjerkw at gmail.com
Wed Jun 21 14:28:35 CEST 2006
The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9.
Other cutoffs may introduce artefacts.
On 6/21/06, Isabella Daidone <i.daidone at caspur.it> wrote:
> Sorry, but I'm a little bit confused about what rvdw to use for
> simulations of proteins in solution with gromos96 force field while using
> pme for
> coulomb interactions.
> In the gromacs 3.3 manual I still read (with pme):
> rcoulomb=rlist=rvdw=0.9 nm
> Then, I found in the discussion list (+ the paper J Comp Chem,
> 1998, 19:535) someone suggesting rvdw=1.4 nm.
> Could you please help me? what's your suggestion?
> Is it nowadays anyway accepted to
> use rcoulomb=rlist=rvdw=0.9 nm?
> And is there any difference between the standard G43a1 version or the
> newest (G53a...)?
> Thank you very much.
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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