Hi, #compchem people!
I would like to do some Markov state analysis for my MD simulations. What are the software tools people use for this these days? I used to use HTMD or PyEmma, but neither of these has been updated in years and they are a bit difficult […] https://mastodontti.fi/@piiabartos/113791761839641425
I would like to do some Markov state analysis for my MD simulations. What are the software tools people use for this these days? I used to use HTMD or PyEmma, but neither of these has been updated in years and they are a bit difficult […] https://mastodontti.fi/@piiabartos/113791761839641425
Comments
https://deeptime-ml.github.io/latest/index_msm.html#
While still depending on PyEMMA, some of the tools have been updated more recently and rewritten for the newer library.
You can find examples at
https://github.com/markovmodel/pyemma-workshop
If you still need a featurizer (depending on which feature space you calculate the MSM in), you can use those from PENSA instead.
https://pensa.readthedocs.io/en/latest/