[gmx-users] GROMACS command for energy calculation

Acoot Brett acootbrett at yahoo.com
Mon Aug 27 00:01:03 CEST 2012

Dear Justin,
In the internet there is the following content. But if I need to measure the non-bonded energy between residues within a protein, or between fragments within a protein, can you advise on how to set up the energygrp?
 Energy group exclusions
Pairs of energy groups for which all non-bonded interactions are excluded. 
An example: if you have two energy groups Protein and SOL, 
energygrp_excl = Protein Protein  SOL SOL 
would give 
only the non-bonded interactions between the protein and the solvent. This is 
especially useful for speeding up energy calculations with mdrun -rerun and for excluding interactions within frozen groups. 

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation

On 8/26/12 5:02 PM, Acoot Brett wrote:
> Dear All,
> After the production MD has been done, does GROMACS has a command which can calculate the interaction energy between any 2 residues in a frame of structure from the MD?

Assuming you have made proper use of energygrps in the .mdp file, you can extract nonbonded terms between these groups from the .edr file using g_energy.  If you have not set energygrps, you can create a new .tpr file and use mdrun -rerun to recalculate the energies from an existing trajectory or snapshot.


-- ========================================

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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