[gmx-users] Energy from a subgroup of molecules

p buscemi pbuscemi at q.com
Wed Apr 10 22:24:15 CEST 2019

Dear Users,
I've performed an adsorption experiment in which a fraction of molecules in solution adsorb to a surface. I can extract the index of those adsorbed, and I can obtain the total interaction ( LJ ) of the energy group with the surface.
I can estimate the average interaction of the adsorbed molecules by dividing the total energy by the number of molecules within a certain distance ( the index number )
How might I use gmx energy to recalculate the interaction using the original surface but only the adsorbed molecules specified in the index file... something like
"gmx energy -f starting.gro -n index.ndx"

A single point calculation would be quite satisfactory.

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