[gmx-users] mdrun -rerun

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 13 22:29:08 CEST 2017


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.


On Thu, Jul 13, 2017 at 9:55 PM Alex <nedomacho at 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:
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list