[gmx-users] on energygrp_excl

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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