msmbuilder-legacy
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msmbuilder
Legacy release of MSMBuilder
The script calculates state populations by calling msm_analysis.get_eigenvectors and requesting only one eigenvalue. I found that this leads to non-convergence issues. Increasing the number of requested eigenvalues (i.e. >= 4)...
So here's what Cluster.py currently says: ``` 11:23:27 - Errors detected in conversion: 92 trajectories 11:23:27 - The trajectories in error are numbers [ 0 2 3 4 5 8...
Hi, I recently noticed 2 potential bugs in the TPT function of MSMExplorer: - Comparing the top pathways generated by MSMExplorer to those found with tpt.py, I see a divergence...
I think we should include simple models where things like TPT, PCCA, MFPT, and eigenvalues can be calculated analytically. We would then use those as unit tests.
Hey, I was wondering if it might be worthwhile to give the PCCA.py script an option to only output MacroMappings.dat, and thus only require a transition matrix as an input....
Would it be useful when calculating implied timescales to also (maybe optionally) save some information on ergodic trimming, specifically the percent of data that is left for each lag time....
I found this to be an issue while building several MSMs of protein conformational change. The state populations were very different from the raw population of each state. I think...
The Voelz lab is currently building MSMs from simulations of non-protein small molecules and peptidomimetics that don't have the usual phi/psi/chi/omega, etc. It would seem easy enough to add user-defined...
I said this on the wiki but wanted to say it here so we can discuss whether it's worthwhile or not. (Also this is something that several of us have...
