[gmx-users] GROMACS command for energy calculation

[Acoot Brett]

Dear All,
 
I am still confused and I hope I can get some detailed explaination. For example, I want to determine the interaction energy between residue 52 and residue 105, how should I set energyggryp and what is the related commands?
 
And if I want to determine the interaction energy between residue 52 in China A and residue 8 in Chain B, what will be the difference?
 
You can also tell me a internet link on it.
 
Cheers,
 
Acoot


----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, 27 August 2012 8:07 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 8:01 AM, 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?

http://www.gromacs.org/Documentation/File_Formats/Index_File

Mark

>  
> 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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