[gmx-users] on energygrp_excl

Acoot Brett acootbrett at yahoo.com
Mon Nov 5 01:46:23 CET 2012

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

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?

I am looking forward to getting your reply.



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