[gmx-users] Domain Decomposition

[Justin Lemkul]

On 11/8/17 12:02 PM, Wes Barnett wrote:
> 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?
>

Simple neighbor searching is required when using infinite cutoffs (e.g. 
gas phase).

The solution is to use OpenMP parallelization, e.g.

mdrun -ntmpi 1 -ntomp X

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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