A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

Bogetti, A.; Leung, J.; Russo, J.; Zhang, S.; Thompson, J.; Saglam, A.; Ray, D.; Abraham, R.; Faeder, J.; Andricioaei, I.; Adelman, J.; Zwier, M.; LeBard, D.; Zuckerman, D. M.; Chong, L.

doi:10.1101/2022.10.04.510803

bioRxiv · 10.1101/2022.10.04.510803

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

Bogetti, A.·Leung, J.·Russo, J.·Zhang, S.·Thompson, J.·Saglam, A.·Ray, D.·Abraham, R.·Faeder, J.·Andricioaei, I.·Adelman, J.·Zwier, M.·LeBard, D.·Zuckerman, D. M.·Chong, L.

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Abstract

We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) path sampling strategy to even larger systems and/or slower processes. The tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of "binless" schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling at the system biology level. Applications of the tutorials range from atomistic to residue-level to non-spatial models, and include complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics simulations and completed the previous suite of WESTPA tutorials.

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Bogetti, A., Leung, J., Russo, J., Zhang, S., Thompson, J., Saglam, A., Ray, D., Abraham, R., Faeder, J., Andricioaei, I., Adelman, J., Zwier, M., LeBard, D., Zuckerman, D. M., Chong, L.. 2022-10-07. A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software. https://doi.org/10.1101/2022.10.04.510803

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