[gmx-users] g_enermat: group.dat file

[Justin Lemkul]

On 2/10/14, 3:59 PM, shivangi nangia wrote:
> Dear Gromacs users,
>
> I have a question regarding the input file group.dat that has to be
> supplied for using g_enemat.
>
> The manual says "With *-groups* a file must be supplied with on each line a
> group to be used."
>
> I need to calculate the interaction energy of each of my protein residue
> (186 residues) with only tail groups of the bi-layer.
>
> I am not sure what exactly to write in the group.dat file: residue numbers?
> atom/bead (CG) name?
>
>
> Will it use the groups I had in the index file that were incorporated in
> the .edr file?
>

What you need are energygrps in the .mdp file.  g_enemat is only a 
post-processing tool for existing energygrps; it cannot decompose nonbonded 
interactions in the way that you want.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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