[gmx-users] defining parameters in a separate itp file

[Dave M]

Hi Justin,

Thanks, I just posted redmine issue #3204.
Will try pull code.

On Thu, Nov 14, 2019 at 6:02 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/12/19 6:30 PM, Dave M wrote:
> > Hi Justin,
> >
> > I am having troubles now with domain decompositions when I use openMPI
> > mpirun but it works fine when I run on single mpi. My system is quite
> large
> > (80x80x80) and I defined additional bonds in top file as:
> >
> >
> > [ intermolecular_interactions ]
> >
> > [ bonds ]
> >
> > ; ai aj type
> >
> > 3123   40767   6   4.0047  1000
> >
> > 812    41625   6   3.7768  1000
> >
> > 1560   42483   6   3.7569  1000
> >
> > 2378   43341   6   4.0945  1000
> >
> >
> >
> > I get error like this:
> >
> >
> > Not all bonded interactions have been properly assigned to the domain
> > decomposition cells
> >
> > A list of missing interactions:
> >
> >         Harmonic Pot. of      8 missing      6
> >
> >            exclusions of     -4 missing     -4
> >
> >
> > I saw an old mail thread where Mark suggests to use
> > [intermolecular_interactions]. Am already doing it but I still get errors
> > (link:
> >
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg37888.html
> >   )
> >
> >
> > I use this:
> >
> > mpirun -np 4 gmx_mpi mdrun  -deffnm 03-run -rdd 2 -ntomp 16
> >
> >
> > With np = 1 it works fine.
> >
> >
> > Would it be possible to overcome this? On single MPI it will take many
> > months to get the job done.
>
> Everything you've posted seems to suggest that the way
> [intermolecular_interactions] are designed to function no longer work
> properly. A bug report/feature request may be appropriate via Redmine.
>
> In the meantime, it looks like your only option is to use the pull code,
> which does play nicely with domain decomposition.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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