[gmx-users] on energygrp_excl
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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