GROMACS version: 2022.4
GROMACS modification: Yes/No CUDA
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I’m running a model with E. coli ATP synthase F0 as the protein embedded in a POPC bilayer.
Currently, I’m using this command
gmx sasa -s ../process_trajectory/protein_popc.tpr -f ../process_trajectory/protein_popc.xtc -n ../process_trajectory/sasa.ndx -o sasa.xvg -or -surface -output
to obtain the sasa for around 50 amino acids in the system. However, it takes me about 7 hours to run it for my trajectory which is 500ns. I checked System Monitor and it is only using one core. My GPU utilisation is also at 0%. I tried running gmx sasa on other trajectories of the same system simultaneously but they all seem to be sharing the same single core. Is it possible for me to run gmx sasa on multiple cores or have gmx sasa running on different terminals use different cores for their operation?