[gmx-users] exclude vdw interactions for pair of residues

Justin Lemkul jalemkul at vt.edu
Mon Sep 24 11:51:54 CEST 2012

On 9/24/12 5:42 AM, Shreyas Supekar wrote:
> Dear gmx-users,
> I have a system of psuedo-atoms immersed in water. I want no vdw
> interactions among the psuedo-atoms but I do need psuesoatom-water
> interactions. Basically I need the psuedo-atoms fixed. I know I can use
> freeze or position restraints to fix them but the number of psuedo-atoms is
> large(~20000) and so its a waste of my computer resources to calculate all
> such psudoatom-psuedoatom nonbonded interactions. Please let me know if any
> such trick exists.

Use energygrps and energygrp_excl in the .mdp file.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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