~7x increase in runtime from 0.15 to 0.16 for explicit calculations

Running the same calculation (e.g. same inputs and yaml files) using yank 0.15.2.dev0 vs 0.16.1 causes the total runtime to increase from ~2.5 days to ~14 days. I’ve looked through the yaml documentation, and I don’t see anything that could have changed from version to version (with the exception of how MPI runs are conducted, but this calculation was done in serial), but have a feeling I’m wrong there. I’ve attached my input files here; am I missing something very obvious, or are the estimated time-to-completions in 0.16 not accurate?

Note: Within the zipfile, the nohup.out is the (limited) output from the 0.16 run, and I’m using the same hardware for both runs (1080 gtx, i7, ~50GB memory)

4LUC.zip.tar.gz

[spadavec]

Just made the change @andrrizzi suggested (kept everything @ 0.16) and it indeed got the total runtime down to <2 days (id put a jeff_goldblum_says_wow.gif here if I had one).

[andrrizzi]

That would work! I think even only rolling back to the openmm in the main channel should bring the total runtime to something close to 3-3.5 days. Alternatively, you can go into the code and substitute this line with

alchemical_factory = mmtools.alchemy.AbsoluteAlchemicalFactory(disable_alchemical_dispersion_correction=True)

This should be even faster than 0.15 and bring the calculation to less than 2days.

I did check the overlap between the expanded cutoff states and the the alchemical state with and without analytical correction for the alchemical atoms, and there was very little difference. The std of the difference of the energies was ~0.015kT (even less for the solvent phase), so I don’t think disabling the analytical correction will affect our free energies much.