[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

Lee Soin nomadoro at gmail.com
Sun Jul 26 17:31:06 CEST 2009

My problem is actually as follows:
I have three groups of atoms: A, B and C. Now I want to keep full
interaction between A-B and A-C, but only retain the repulsive part of VDW
interaction between B-C. I'm using the OPLS force field. It seems to me that
the parameters for OPLS in the .itp files are specified for each atom, so is
there any way to treat the interaction pairwise?

2009/7/26 Mark Abraham <Mark.Abraham at anu.edu.au>

> Lee Soin wrote:
>> Hello!
>> I've read from the manual that the mdp option energygrp_excl can exclude
>> pairs of energy groups for non-bonded interactions. But now I would like
>> to
>> remove all other non-bonded interactions but retain the repulsive part of
>> the VDW interaction for a pair of energy group. Is there a way to do so?
> Use grompp -pp to get a fully preprocessed .top file, and edit that to zero
> all the charges and dispersive LJ parameters.
> Mark
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Department of Physics
Nanjing University, China
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