[gmx-users] Cutoff Parameters

Soumik Banerjee soumik_banerjee at yahoo.co.uk
Wed Nov 19 12:11:06 CET 2008


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. 


Soumik BanerjeeMax-Planck-Institute
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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