[gmx-users] Switching Group to Verlet

[Mahmood Naderan]

OK thank you very much. I got it.

I ran

bin/gmx_mpi grompp

and it rebuilds the tpr file. Then I verified that binary tpr and saw the
Verlet. Then I ran

mpirun -np 4  bin/gmx_mpi mdrun -v -ntomp 2

without any error.

Thanks.


Regards,
Mahmood



On Fri, Oct 21, 2016 at 5:02 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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