msmbuilder-legacy
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msmbuilder
Legacy release of MSMBuilder
Hi, I would like to validate a MSM with the Chapmam-Kolmogorov test. However, I have some doubts on how to proceed. I think that I should use msm_analysis.propagate_model.py But how...
Hi all: I want to use MSMBuilder2.8.2 to construct a Markov state model to study the protein folding with 150 discrete trajectroy. After the cluster step with hybrid method,I got...
This old functionality is not there anymore -- I need to put it back in.
I'm trying to get this script to work, and found a few problems. Here are proposed solutions: (1) the first few lines have outdated variable names (CamelCaps) and routines. They...
Awhile back @rmcgibbo and @schwancr wrote a script for me which saves structures from given states, but also provides the path back to the raw data for what RUN, CLONE,...
In the line 386 of this script, 'row[s] = 0', this simply changes the element the matrix c as well. It will lead to this self-transition counts missing in the...
No matter what argument you pass for --replacement, the script reports (and uses) the value 'True'. If I change the argument type from 'bool' to 'int' and pass 0 or...
Suppose I perform dihedral clustering and MSMBuilder reports that the cluster radius is 1.8. What are the units here? I know that the the angles phi_i get projected 2-fold onto...
In the PCCAPlus class from `lumping.pcca_plus`, the `optimize_A` method uses Scipy's `optimize.anneal` method. This is deprecated in SciPy v0.14.0 version, and it uses `optimize.basinhopping` instead. Scipy returns a couple warnings...
