[gmx-users] Energygrps

Justin Lemkul jalemkul at vt.edu
Tue Feb 20 18:32:16 CET 2018

On 2/20/18 5:49 AM, Ahmed Mashaly wrote:
> Hi
> What is the default engerygrps to be written if I don't specify them in the mdp file?

The default behavior is to not decompose the energy in any fashion, and 
just report it for the whole system.

> And if I have more than one ligand and want to calculate the energy between them and the protein, and also between one part of the protein (loop) and the rest of the protein I should make an index identifying each ligand indvidually and this part too and my energygrps will be protein lig1 protein lig2 protein loop ...

A real snippet of an .mdp would be good here, because it appears you're 
just repeating groups, which is not appropriate. If you want the 
interaction of a ligand with a protein, use:

energygrps = Protein LIG

If there are multiple groups to consider:

energygrps = Protein LIG1 LIG2

A full matrix of all possible combinations will be generated. Whether or 
not this quantity means anything within a given force field is another 
matter, but I'm a broken record in saying that nearly every day on this 

> If I don't specify this from the beginning is it the same to get with mdrun rerun or will be different? This

Yes, this is the main purpose of mdrun -rerun. There is no need to bog 
mdrun down with such energy decomposition because the physics doesn't 
depend on it. Treat it as analysis and just get the values by 
post-processing the trajectory.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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