bioRxiv version 5

Updated manuscript from proofs.

bioRxiv version 4

• The ./reproduce.sh script has been re-run and all figures have been replaced with the results.
• Minor updates for journal submission.

bioRxiv version 3.1

• Added new figure illustrating analysis for reduced potential
• Some manuscript revisions to incorporate referee feedback and feedback from others

JCTC submission version 1

This release corresponds to the version of the code and manuscript submitted to JCTC.

bioRxiv version 2

This release corresponds to the version of the code used to generate all figures in the manuscript automatically for bioRxiv version 2.

Major changes:

• Incorporated useful feedback from Wei Yang (FSU) and Michael Gilson (UCSD). (Thanks!)
• Data now stored in NetCDF format.
• Fixed a bug in figure plots where simulation times were incorrectly reported.
• Fixed a bug in integrator where the default OpenMM Langevin integrator was used instead of the intended VVVR.
• Simplified all parameters to be simple multiples of natural relaxation time $\tau$.
• All simulation times now reported in reduced (dimensionless) units of natural relaxation time $\tau$.
• Minor manuscript and figure edits and improvements.

bioRxiv version 1

This release corresponds to the version of the code used to generate all figures in the manuscript automatically.