[gmx-users] Domain Decomposition

Wes Barnett w.barnett at columbia.edu
Wed Nov 8 18:03:01 CET 2017

On Wed, Nov 8, 2017 at 11:11 AM, Shraddha Parate <parateshraddha at gmail.com>

> Dear Gromacs Users,
> I was able to achieve a spherical water droplet without periodic boundary
> conditions (PBC) by changing few parameters in the .mdp files as below:

> However, I am facing the following error:
> *Fatal error:*
> *Domain decomposition does not support simple neighbor searching, use grid
> searching or run with one MPI rank.*
> I tried adding the '-nt 1' in the command for mdrun but it consumes 2 weeks
> for a 1 ns simulation since it utilizes only 1 CPU.
> Is the error occurring because of changes in .mdp file parameters? Is there
> any other way to make some changes in the mdrun command to make the
> simulation faster?
> Thank you in advance.
> Best regards,
> Shraddha Parate

The error indicates you should try changing how neighbor searching is done.
Have you tried that?

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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