[gmx-users] mdrun -rerun

[Alex]

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
>> > > > --
>> > > > Gromacs Users mailing list
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>
>