# Your system is not well equilibrated in NVT mdrun

**URL:** <https://gromacs.bioexcel.eu/t/your-system-is-not-well-equilibrated-in-nvt-mdrun/11837>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [March 29, 2025, 9:04am UTC](https://gromacs.bioexcel.eu/t/your-system-is-not-well-equilibrated-in-nvt-mdrun/11837 "2025-03-29T09:04:58Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![sizhe\_Li](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sizhe\_Li](https://gromacs.bioexcel.eu/u/sizhe_Li)\
**Post date:** [March 29, 2025, 9:04am UTC](https://gromacs.bioexcel.eu/t/your-system-is-not-well-equilibrated-in-nvt-mdrun/11837/1 "2025-03-29T09:04:58Z")

</div>

## When I try to use: gmx mdrun -deffnm \*\_nvt -nb gpu It show me:

Program: gmx mdrun, version 2024.4  
Source file: src/gromacs/ewald/pme\_redistribute.cpp (line 305)  
MPI rank: 3 (out of 8)

Fatal error:  
2 particles communicated to PME rank 3 are more than 2/3 times the cut-off out  
of the domain decomposition cell of their charge group in dimension x.  
This usually means that your system is not well equilibrated.

## For more information and tips for troubleshooting, please check the GROMACS website at [Common errors when using GROMACS - GROMACS 2025.4 documentation](https://manual.gromacs.org/current/user-guide/run-time-errors.html)

I have changed some em.mdp and nvt.mdp like this:  
em.mdp:  
; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 500.0 ; Stop minimization when the maximum force \< 10.0 kJ/mol  
emstep = 0.01 ; Energy step size  
nsteps = 500000 ; Maximum number of (minimization) steps to perform

nvt.mdp:  
; Run parameters  
integrator = md  
nsteps = 500000  
dt = 0.001  
; Output control  
nstenergy = 5000 ; save energies every 1.0 ps  
nstlog = 1000 ; update log file every 1.0 ps  
nstxout-compressed = 1000 ; save coordinates every 1.0 ps  
tc-grps = system  
tau\_t = 1