Thank you for the pointers! I indeed got some minor improvements from increasing ‘nstlist’ to 400. I was also able to reduce the number of CPUs used per run without impacting performance much. Thank you!
I tested the v-rescale thermostat and indeed that alone raises my performance to ~52ns/d!
I guess the big question is really what implications the use of the v-rescale thermostat would have on my system. I’m using the Charmm36ff. Almost all papers I’ve seen prefer the use of Nose-Hoover with the Charmm36ff. There are however several publications using the GROMOS 54A7 ff with the v-rescale thermostat.
- Does the choice of thermostat depend on the forcefield? If so, why?
Justin Lemkul in his tutorial mentions the greater (membrane) fluctuations allowed by Nose-Hoover. Do you think I could get away with using the v-rescale thermostat as I’m primarily interested in the dynamics of my protein-ligand system?