production() runs 1ns at a time, and uses timeseries.detectEquilibration() to determine whether the simulation has converged to within a predefined (0.0001 g/mL) standard error.
equilibrate() is an optional fixed-length equilibration step. If run, this is in addition to (not instead of) timeseries.detectEquilibration() checking for convergence.
Further addresses discussion from https://github.com/choderalab/TrustButVerify/issues/7#issuecomment-55505375
Primary changes: