[gmx-users] GROMACS command for energy calculation

[Acoot Brett]

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?
 
Cheers,
 
Acoot
 Energy group exclusions
energygrp_excl:  
Pairs of energy groups for which all non-bonded interactions are excluded. 
An example: if you have two energy groups Protein and SOL, 
specifying 
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>
Cc: 
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

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

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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