[gmx-users] mdrun -rerun

[Alex]

Here you are, as run on the production tpr:

$ gmx make_ndx -f prod.tpr
GROMACS:    gmx make_ndx, VERSION 5.0.5

........
........

Reading structure file
Reading file prod.tpr, VERSION 5.0.5 (single precision)
Going to read 0 old index file(s)
Analysing residue names:
There are:   208      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System              :  6537 atoms
  1 Other               :  6537 atoms
  2 BUT                 :    84 atoms
  3 CBD                 :    53 atoms
  4 DEC                 :  6400 atoms


On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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