There are lots of discussions on this topic in the list archive. See, for
example:
http://www.gromacs.org/pipermail/gmx-users/2002-August/002320.html
-Justin
Soumik Banerjee wrote:
Hi,
I am sorry that I am repeating an earlier email that I sent out to the
list. I did not receive a reply. It would indeed be very useful for me
to have some input on this.
I am new to gromacs and have a pretty basic question. I am using
gromacs-3.3.3 to simulate glycine crystal growth. My system consists of
glycine crystal surrounded by a solution of glycine in water (system
size: 4.28 by 5.76 by 3.27 nm^3). I have been trying to find appropriate
values for the cutoff distances (rvdw, rcoulomb) and corresponding
rlist. I use GROMOS96 43a1 force field with PME (pme_order = 4, rtol =
1e-5).
The examples given in the gromacs tutorial use rvdw = rlist = rcoulomb =
0.9 (with coulombtype = cutoff). I also found a couple of relevant
journal articles that used these parameters. A relevant message on the
archive
(http://osdir.com/ml/science.biology.gromacs.user/2006-06/msg00389.html)
suggests the use of these parameters. Also, "Using PME" on page 78 of
the manual 3.3 suggests rvdw = rlist = rcoulomb = 0.9
However, the manual suggests rvdw = 1.4 for grmos96 force field. When I
did a gmx-users list search, I found some mdp files from various users
that use vdw = rlist = rcoulomb = 0.9/1.0.
Based on sections 7.3.9 and 7.3.10, I think rlist = rcoulomb = 0.9, and
rvdw = 1.4 would be appropriate. However, I am not completely sure and
it would be great if someone can please recommend a set of values for
these parameters (rlist, rvdw, rcoulomb) for coulombtype = PME.
Best,
Soumik
*Soumik Banerjee
*
Max-Planck-Institute
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Germany
Email: [EMAIL PROTECTED]
Phone: +49 391 6110 163
<http://www.esm.vt.edu/murg>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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