[gmx-users] mdrun -rerun

[Alex]

Hi Mark,
That's the problem: the names are exactly as they appear whenever atom
group selections are made... Any thoughts?
My topology is as clean as it gets:

#include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"
#include "but.itp"
#include "cbd.itp"
#include "decane.itp"

[ system ]
; Name


[ molecules ]
; Compound        #mols
BUT               7
CBD               1
DEC               200

On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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