[gmx-users] Energy from a subgroup of molecules

Mark Abraham mark.j.abraham at gmail.com
Thu Apr 11 08:48:29 CEST 2019


You can't do that with gmx energy, as you need mdrun to understand the new
grouping. But making a new .tpr with the energy groups so defined permits
you to use gmx mdrun -rerun for such a single point energy evaluation.


On Wed., 10 Apr. 2019, 22:24 p buscemi, <pbuscemi at q.com> wrote:

> 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.
> thanks
> Paul
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