# Error in md run

**URL:** <https://gromacs.bioexcel.eu/t/error-in-md-run/7649>\
**Category:** User discussions\
**Created:** [November 15, 2023, 7:43am UTC](https://gromacs.bioexcel.eu/t/error-in-md-run/7649 "2023-11-15T07:43:12Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\
**Post date:** [November 15, 2023, 7:43am UTC](https://gromacs.bioexcel.eu/t/error-in-md-run/7649/1 "2023-11-15T07:43:12Z")

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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)

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<div class="post-metadata">

**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [November 15, 2023, 2:03pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run/7649/2 "2023-11-15T14:03:02Z")

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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.

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<div class="post-metadata">

**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\
**Post date:** [November 17, 2023, 1:18am UTC](https://gromacs.bioexcel.eu/t/error-in-md-run/7649/3 "2023-11-17T01:18:17Z")

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Thank you for your suggestions!