[gmx-users] COMM and WCA

Berk Hess gmx3 at hotmail.com
Fri Dec 12 08:32:51 CET 2008


You can not construct a WCA potential in Gromacs
by using LJ with a certain cut-off.
The cut-off with vdwtype=cut-off is the LJ neighborlist
cut-off, NOT the interaction cut-off.
To construct a WCA potential you have to use user tables.
There is one inconvience here:
if you have multiple sigma_ij's, you need a separate table
(energygrp_table) for every sigma_ij.


Date: Thu, 11 Dec 2008 23:10:02 +0530
From: manik.mayur at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] COMM and WCA

I was wondering if there is any way to:
1) COMM removal in a specific dimension just life freezedim. e.g. I want COMM removal in y-direction only.
2) Get WCA potential by setting [vdw-type: Shift] and [rvdw=2^(1/6)*sigma]; As in WCA the repulsive part of LJ is retained by setting the cutoff radius as 2^(1/6)*sigma and shifting it by epsilon. If not, can I get some literature/reference on how VdW's is implemented in GROMACS including the role of rvdw-switch.


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