jalemkul at vt.edu
Tue Feb 20 18:32:16 CET 2018
On 2/20/18 5:49 AM, Ahmed Mashaly wrote:
> 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.
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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