Hi, As with any index group, you can make them with gmx make_ndx, gmx select, or your favourite text editor, and feed them to gmx grompp -n. You normally get spoiled with automatically generated groups that happen to match moleculetypes and such. So probably you have SOL already.
Mark On Thu, Jul 13, 2017 at 9:55 PM Alex <nedoma...@gmail.com> wrote: > Hi all, > > I have a system that a subsystem of interest (molecules BUT and CBD) and > the solvent (DEC). I have simulated it and have a trajectory. > > I would like to find out the total energy of interaction between BUT and > CBD as a function of simulated time, so my thought is to do -rerun and > exclude the interactions in the following group pairs: > > DEC-DEC > BUT-BUT > CBD-CBD > DEC-BUT > DEC-CBD > > When setting energygrp-excl with the following pairs, I immediately get a > grompp error saying that DEC isn't an energy group. Since I've never done > this before, can you please share your wisdom? > > Thank you, > > Alex > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.