Hi,
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. 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. Also, "Using PME" on
page 78 of the manual 3.3 suggests rvdw = rlist = rcoulomb = 0.9
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 BanerjeeMax-Planck-Institute
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Germany
Email: [EMAIL PROTECTED]
Phone: +49 391 6110 163
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