[gmx-users] Cutoff Parameters

Soumik Banerjee soumik_banerjee at yahoo.co.uk
Tue Dec 2 11:19:47 CET 2008


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. 


Soumik Banerjee
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Email: banerjee at mpi-magdeburg.mpg.de
Phone: +49 391 6110 163 

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