[gmx-users] Domain Decomposition
jalemkul at vt.edu
Wed Nov 8 18:04:26 CET 2017
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>
>> 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.
The solution is to use OpenMP parallelization, e.g.
mdrun -ntmpi 1 -ntomp X
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
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jalemkul at vt.edu | (540) 231-3129
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