[gmx-users] GROMACS command for energy calculation

[Justin Lemkul]

On 8/26/12 6:01 PM, Acoot Brett wrote:
> 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?
>

You can use whatever custom energygrps you want, supplied with an index file. 
Note that you don't necessarily need energygrp_excl to calculate interaction 
energies between molecules or fragments, you just need energygrps.  If you're 
breaking molecules apart, it's especially difficult to use energygrp_excl 
(depending on the algorithms used), and the speedup probably isn't worth it.  A 
rerun should only take a matter of hours, even for a rather long trajectory.

-Justin

> 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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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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