msmbuilder

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Hi, When I'm running the timescale.py in the TemplateProject MSM folder, I got this error multiple times: `Intel MKL ERROR: Parameter 5 was incorrect on entry to DGEEV.` `ValueError: Internal...

lenhsherr

Macrostate or microstate structure and Transition Pathways ?

26

I was recently trying to analyze a series of MD simulation trajectories using the MSMBuilder and I encountered the following problems: 1) how can I obtain the representative structures of...

Avon07

[question] how to distill intermediate structures from MSM ?

1

after I finishing constructing MSM model for my trajectories and system, how can I distill the structures of the corresponding microstate/macrostate ? according to the protocol, a sample trajectory from...

Nidane

MacroAssignments_ and labels_ are NoneType object while using APM.

1

Hi, I am trying to use APM to cluster my featurized trajectories, for a set of parameters, even though it seems to be working fine, the cluster object does not...

zshamsi2

GaussianHMM parameter estimation runs indefinitely

1

I am able to generate an HMM in a few seconds whenever I have 1 million or fewer datapoints in my list of trajectories. If I have 2.7 million points...

tmaula

inspiration: https://garstats.wordpress.com/2017/11/28/trimmed-means/

cxhernandez

No lumping in msmbuilder website?

1

I use the msmbuilder.org website quite a lot to quickly refer to the docs. However, I've seen that there is no information on the `msmbuilder.lumping` package. However I've seen that...

jeiros

e.g. scalers, dihedral featurizers, etc.

cxhernandez

Version 3.9 release schedule

4

Target: end of June

brookehus

pinging @liusong299 The success of APM tests seems heavily dependent on this [random_state](https://github.com/msmbuilder/msmbuilder/blob/master/msmbuilder/cluster/apm.py#L222) being set to zero. Please review this code, and provide a more reproducible test; otherwise, it will...

cxhernandez