Tim Hempel

Can you specify, what is "quite different"? In case the MFPT is extremely high compared to your observation, maybe the MSM is not connected - you may want to double-check...

Sorry, my fault. I'm actually calling ```python bmsm.set_model_params(samples=[pyemma.msm.markov_model(p) for p in samples]) ``` after instantiating it. This overwrites the `dt_model='1 step'` to default.

I agree, but wouldn't it just be fixed by setting the defaults in this method to None?

Hi, I tried to explain that in an older issue, maybe that helps? https://github.com/markovmodel/PyEMMA/issues/1533#issuecomment-1015395843

Depending on how how large your protein is, taking distances between all heavy atoms yields a very high-dimensional space - however, you may imagine that this space also contains a...

That sounds like your states are not connected, i.e., that you are not sampling both opening and closing transitions. That would be a possible reason for point 1 (MSMs give...

Let me give an example: Two systems A and B that have partially overlapping discrete states with trajectories `dt_A = [0, 1, 2, 1, 0]` and `dt_B = [1, 2,...

Maybe you want to look into the objects that you are plotting - what are the predictions and estimates of the CK-test, in numbers? That should help you to debug...

Probably related to #1324.

I just looked into your data. Indeed, this is the issue we are discussing here. Until it is fixed, you might want to use maximum likelihood HMMs to conduct model...