[gmx-users] g_enermat: group.dat file

Justin Lemkul jalemkul at vt.edu
Mon Feb 10 22:24:52 CET 2014

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 A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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