Hi, 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.
Mark On Wed., 10 Apr. 2019, 22:24 p buscemi, <[email protected]> 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
