Tim Hempel
BHMM CK-test
The CK-test for BayesianHMMs gives me a cryptic index error in the case that the original estimate is done on an active set smaller than the full set of states....
When setting up models from an existing transition matrix, using the `dt_model` in a regular ML MSM and in a sampled MSM yields different scaling. ```python bmsm = pyemma.msm.models.SampledMSM(P=tmat, dt_model='0.1...
The link to the Webserver doesn't work without https (tested with safari & chrome on Mac), this should fix it :)
Using `mdconvert` from the command line produces some unexpected behavior for converting DCD to XTC format. It seems to be limiting the time field to a max number of 999,...
Hi, first let me thank you for this great project! It's super helpful. I'm not 100% sure what the problem is, but when I install openmmforcefields via `conda install -c...
Unit tests fail when running them on my local resource, apparently some paths are not well configured. I get the following errorwith test_simple_wrapped.py and test_simple_wrapped.py: IOError: [Errno 2] No such...
PyEMMA's support for python 2 will soon expire (also, python 2's end of life is coming closer). That means that we need python 3 support.
Using one's own generator class, i.e. for implementing a pyemma analysis script, does not work as described in notebook 5. First, their are several bugs in the notebook itself. Substituting...
This is the documentation on how to add existing trajectories. It includes a few fixes that were necessary: - For multiple engines in a pyemma analysis, file names have to...
For actual adaptive simulations, a flexible way to analyze the data is very important. Apart from choosing input parameters such as the lag time and msm states, it will be...