Dear GROMACS users,
I am running 24-replica REMD simulations using GROMACS 2023 on our local cluster.
Each node has 48 cores and I launch the job as shown below:
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export OMP_NUM_THREADS=1
for i in {0..23}; do
mpirun -machinefile $PBS_NODEFILE -np 48 \
/apps/codes/gromacs/2023/bin/gmx_mpi convert-tpr \
-s replica_$i/remd_61_65.tpr -extend 5000 -o replica_$i/remd_66_70.tpr
done
mpirun -np 48 /apps/codes/gromacs/2023/bin/gmx_mpi mdrun \
-multidir replica_{0..23} \
-s remd_66_70.tpr -deffnm remd_66_70 -cpi \
-replex 1000
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Inside the *.log* files of the replicas, the reported performance is:
(ns/day) Performance: 3.11
So I expected that each 5 ns extension would finish in about **1.6 days**.
However in practice, the job takes **15–20 days** of wall-clock time to finish, which is far slower.
Any guidance on how to run REMD more efficiently would be greatly appreciated.
Best regards,
Sankar Maity
NIT ROURKELA