[gmx-users] on energygrp_excl

Justin Lemkul jalemkul at vt.edu
Mon Nov 5 02:13:44 CET 2012

On 11/4/12 7:46 PM, Acoot Brett wrote:
> Dear All,
> I have a protein composed of chain A and chain B. I want to determine the interaction energy between chain A and chain B. Is it the following energygrp_excl correct or not?
> energygrp_excl=chain A chain A chain B chain B SOL SOL chain A SOL chain B SOL

Using exclusions like this prevents nonbonded interactions from being calculated 
between these groups; the exact opposite of what you want.

> Or is it tool long? I see from the on-line tutorial the energygrp_excl only contains 4 parameters, for example
> energygrp_excl=Protein Protein SOL SOL
> In addition, for the energy calculated by g-energy, does it contain the hydrogen bond energy and the salt bridge energy, or does gromacs regard hydrogen bond energy and the salt bridge energy as bonded energy or non-bonded energy?

There are no discrete energy terms for hydrogen bonds or salt bridges.  These 
are all lumped into Coulombic terms.

To achieve what you want, all you need is:

energygrps = Chain_A Chain_B

Whether or not the resulting numbers are useful (especially when using PME, a 
topic discussed at length in previous posts to this list), is up to you to 
demonstrate.  But this is how you can acquire the desired energy terms.



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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