Gromacs mpi run command

User discussions
1

GROMACS version:2022.3

I am trying to continue my simulation on an HPC cluster using gmx_mpi mdrun with -cpi and -append.
However, when I use the restart command, I get an error .

Here is the command I used:

srun --mpi=pmix_v3 -n 16 gmx_mpi mdrun
-s /nlsasfs/home/biomol/alifaz/bn_rep1_full.tpr
-deffnm bt_rep1_full
-cpi bt_rep1_full.cpt
-append
-nsteps 428733500
-v -ntomp 16

I want to confirm if this is the correct way to restart the simulation.
Could you please tell me:

  1. Is the command written correctly for continuing a run?

  2. Do I need both -cpi and -append, or only one of them?

  3. Is adding -nsteps in a continuation run correct?

2

Hi @gq0067

So

  • -append should be automatic, you can re-enforce it, but you do not need it;
  • -cpi is mandatory if you want to continue from a checkpoint file without recompiling a tpr file;
  • the -nsteps should overwrite the number of steps inside the tpr file, so these shouldn’t cause any problems but just force your simulation to go on up to when the number of steps is reached (or the simulation stops beforehand).

The command seems overall fine. How is it failing? Can you post the error?