[gmx-users] mdrun -rerun

Thu Jul 13 23:10:56 CEST 2017

Hi,

Your input to gmx grompp -c is some other file though, and that's the set
of index groups that matter, and the default ones should include those
found by gmx make_ndx.

Mark

On Thu, Jul 13, 2017 at 11:06 PM Alex <nedomacho at gmail.com> wrote:

> Same error in v. 2016.1.
>
> On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedomacho at gmail.com> wrote:
>
> > 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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