Incorrect runtime generated by BSS.Protocol.FreeEnergy.()

[Roy-Haolin-Du]

Hi there,

Thanks for these excellent tutorials, but a minor error is incorrect about runtime generated by BSS.Protocol.FreeEnergy()

When I set this in ABFE section:

BSS.Protocol.FreeEnergy(runtime=6*BSS.Units.Time.nanosecond, 
                                      timestep=2*BSS.Units.Time.femtosecond, 
                                      lam_vals=lam_vals_release_restraint, 
                                      perturbation_type="release_restraint")

The runtime should be 6 ns. However, the somd.cfg file gives:

ncycles = 15000
nmoves = 250
ncycles_per_snap = 4
buffered coordinates frequency = 0
timestep = 2.00 femtosecond

which runtime = ncycles x nmoves x timestep = 7_500_000 fs = 7.5 ns
I noticed that the generation runtime is alwasy larger 1.25 fold than what we had set.

So，just kindly hope you can check it.

Thanks a lot.

Best,

[fjclark]

Hi Roy, thanks for raising.

I've created a PR which fixes this: OpenBioSim/biosimspace#390.