[gmx-users] Cutoff Parameters

[Justin A. Lemkul]

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: banerjee at mpi-magdeburg.mpg.de
> 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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