GROMACS version:GROMACS 2020.4-GPU
GROMACS modification: Yes/No
Hi,
I am new for GROMACS, and doing 100ps NVT equilibration of a glycated SARS-CoV2 spike protein in explicit water (total number of atoms 674050). Below is my bash script:
#!/bin/csh
#SBATCH -o slurm.%N.%j.out
#SBATCH -e slurm.%N.%j.err
#SBATCH -p dhvi-md-gpu
#SBATCH --gres=gpu:1
module load GROMACS/2020-4-GPU
gmx_mod grompp -f eq_nvt-SARS.mdp -c eq_npt-SARS.gro -r eq_npt-SARS.gro -p topol.top -o eq_nvt-SARS.tpr -maxwarn 28 -n index.ndx
gmx_mod mdrun -nb gpu -deffnm eq_nvt-SARS
and below is time taken to finish above job:
Core t (s) Wall t (s) (%)
Time: 26885.277 2444.177 1100.0
40:44
(ns/day) (hour/ns)
Performance: 3.535 6.789
Even though using GPU, speed of calculation is very low, and I want to increase the speed.
Anyone please suggest how I can use the maximum efficiency of GPU calculation.
Thanks