Codes written by Samik Bose to
(i) build the Markov state models from WEPY (REVO) data,
(ii) extract the TS ensembles with REVO-MSM,
(iii) estimate properties (MFPT, committors etc) of the MSM.
The objective of the repo is two-fold:
(i) publicly produce the codes of the workflow mentioned in the recently published JACS paper (https://chemrxiv.org/engage/chemrxiv/article-details/64d67c83dfabaf06ff1e8ead).
(ii) the codes are written with the target of understanding/building the REVO-MSM workflow without much consideration of the computational efficiency at this point. Hence one can definitely make it more efficient.
Prerequisite softwares:
(i) Latest version of WEPY (https://github.com/ADicksonLab/wepy)
(ii) Latest version of CSNAnalysis (https://github.com/ADicksonLab/CSNAnalysis)
(iii) Latest version of geomm (https://github.com/ADicksonLab/geomm)
(iv) Deeptime (https://deeptime-ml.github.io/latest/index.html)