[gmx-users] Switching Group to Verlet

[Mark Abraham]

Hi,

What's the question? The function of that switch is to do exactly what you
observe :-) See
http://manual.gromacs.org/documentation/2016/install-guide/index.html#building-only-mdrun
There's
very little value in gmx_mpi that isn't served by mdrun_mpi.

Mark

On Fri, Oct 21, 2016 at 3:14 PM Mahmood Naderan <mahmood.nt at gmail.com>
wrote:

> Meanwhile, I have been confused with one thing!
> If I build Gromacs with -DGMX_BUILD_MDRUN_ONLY=on, then I cannot see
> gmx_mpi.
> On the other hand, if I remove that switch, then I see gmx_mpi but there no
> mdrun_mpi.
>
> Can you please clarify that or give me the right document for that. The
> documentation is really rich and that is confusing for a starter :(
>
>
> Regards,
> Mahmood
>
>
>
> On Fri, Oct 21, 2016 at 4:33 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > No, that's not general. Your approach is right - edit your .mdp file and
> > re-run grompp. Just pay closer attention ;-)
> >
> > Mark
> >
> > On Fri, Oct 21, 2016 at 2:49 PM Mahmood Naderan <mahmood.nt at gmail.com>
> > wrote:
> >
> > > OK. I verified that the cutoff parameter inside the trp file is Group
> > >
> > > mahmood at cluster:gromacs-5.1$ ./bin/gmx_mpi dump -s ~/LPN/topol.tpr |
> > grep
> > > cutoff
> > > ...
> > > Note: file tpx version 83, software tpx version 103
> > >    cutoff-scheme                  = Group
> > >
> > >
> > >
> > >
> > >
> > > Now, according to this reply (by you Mark)
> > > https://www.mail-archive.com/gmx-users@gromacs.org/msg63038.html, it
> > > *should be* possible to overwrite the cutoff parameter of the binary
> file
> > > as I run the mdrun_mpi (similar to nsteps).
> > >
> > > Could you please tell me, what is the correct option for that? I didn't
> > > find any relevant option for mdrun_mpi.
> > >
> > >
> > >
> > >
> > >
> > > Regards,
> > > Mahmood
> > > --
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