[gmx-users] mdrun -rerun

[Mark Abraham]

What does gmx make_ndx think?

Mark

On Thu, Jul 13, 2017 at 10:34 PM Alex <nedomacho at gmail.com> wrote:

> 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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