[gmx-users] Change only one atom pair VdW interaction

Mark Abraham mark.abraham at anu.edu.au
Sat Mar 7 09:40:52 CET 2009

----- Original Message -----
From: Gaurav Chopra <gauravchopra at gmail.com>
Date: Friday, March 6, 2009 19:08
Subject: [gmx-users] Change only one atom pair VdW interaction
To: gmx-users at gromacs.org

> Hello,
> I wanted to know if one can change the VdW epsilon for just one atom pair. If suppose my system has only carbons, hydrogen and oxygen and if I just want to change the epsilon for C-O interaction for VdW without effecting anything else, i.e. not changing C-C interaction for the oplsaa forcefield, is there a way to do this without modifying the code? As epsilon_H = 0, the only thing which will be effected by changing epsilon_C would be C-O and C-C interaction, but I do not want to change C-C interaction but only C-O interaction.

The mechanism for this stuff varies from force field to force field, but you should start with a thorough knowledge of chapter 5 - knowing how your force field is constructing and/or reading parameters from the .itp files. I think all force fields will let you simply specify non-bonded parameters in your [molecule] sections that will override the ones that would otherwise be looked up from the .itp files.


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