[gmx-users] Domain Decomposition

[Wes Barnett]

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

> 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
http://wbarnett.us