The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9. Other cutoffs may introduce artefacts.
Ciao!
Tsjerk
On 6/21/06,
Isabella Daidone <[EMAIL PROTECTED]> 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.
Isabella
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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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