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 2025.1 documentation
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