choderalab/TrustButVerify — pull request #10 by juliebehr (2014-09-17 18:26:19+00:00)
Title: use detectEquilibration to determine length of production

Further addresses discussion from https://github.com/choderalab/TrustButVerify/issues/7#issuecomment-55505375

Primary changes:
* 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.