Error in md run

User discussions
1

GROMACS version:2021.5
GROMACS modification: Yes/No
Here post your question :
Dear users:
The error occured when I had a npt.mdp run. What I can do under this situation?
Command line:
gmx mdrun -v -deffnm npt

Compiled SIMD: AVX2_256, but for this host/run AVX_512 might be better (see
log).
Reading file npt.tpr, VERSION 2021.5 (single precision)

NOTE: Parallelization is limited by the small number of atoms,
only starting 12 thread-MPI ranks.
You can use the -nt and/or -ntmpi option to optimize the number of threads.

Changing nstlist from 15 to 100, rlist from 2 to 2

Using 12 MPI threads
Using 2 OpenMP threads per tMPI thread

WARNING: This run will generate roughly 58315 Mb of data

starting mdrun ‘Great Red Owns Many ACres of Sand’
600000000 steps, 600000.0 ps.
step 41100, will finish Wed Nov 22 21:55:53 2023vol 0.76! imb F 212% 281%

Program: gmx mdrun, version 2021.5
Source file: src\gromacs\domdec\cellsizes.cpp (line 143)
MPI rank: 0 (out of 12)

Fatal error:
The X-size of the box (4.309420) times the triclinic skew factor (1.000000) is
smaller than the number of DD cells (4) times the smallest allowed cell size
(1.078174)

2

Hi, this just indicates that you’re using too many CPUs for the size of your system. It seems though that this happens after a short while, and not at the very beginning, so my guess is that your box is shrinking over time. If your box size/shape changes, then the initial decomposition of the box into domains might not be optimal anymore.

If it’s just a small change due to density equilibration that brings the box below the minimal allowed size, then either use fewer CPUs or make the box slightly bigger.

3

Thank you for your suggestions!