[gmx-users] mdrun -rerun

[Mark Abraham]

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 <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:
>
> 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
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