automatic-equilibration-detection

Automatic detection of equilibrated regions of molecular simulations

A preprint manuscript of this work is available on bioRxiv.

Manifest

• examples/ - code to generate simulation data and figures used in the manuscript
• manuscript/ - the manuscript source and figures
• references/ - some references cited in the paper

Reproducing the results

• Check out a copy of this repository, or download a release corresponding to the version of the paper of interest.
• Go to examples/liquid-argon/ and check the README.md for instructions on running the ./reproduce.sh script.

Automatically computing equilibration times

To detect equilibration start times in your own code, you can use the detectEquilibration() method in the timeseries module of pymbar.

You can install pymbar via the conda package manager:

conda install -c omnia pymbar

and then use the detectEquilibration() method:

from pymbar import timeseries
[t0, g, Neff_max] = timeseries.detectEquilibration(A_t)
A_t_equlibrated = A_t[t0:]

where A_t is the observable timeseries and t_0 is the beginning of the equilibrated region.

The equilibration.py module provided in this repo also provides a stand-alone implementation of this feature with a broader choice of methods for computing integrated autocorrelation times.