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
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