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

[Dave M]

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.


Thanks.

Dave

On Sun, Nov 10, 2019 at 5:35 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/10/19 4:53 AM, Dave M wrote:
> > Hi Justin,
> >
> > I just found that using bond type 6 (instead of 1) works for my test
> > models. So something like this in top file works fine which is bit neat
> and
> > easier to handle for multiple molecules (compared to pull code).
> >
> > [intermolecular_interactions]
> >
> >   [ bonds ]
> >
> >      1     158     6  0.4  1000
> >
> > Just thought to reply what worked for me for future users.
>
> Excellent; thanks for reporting back!
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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