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estimating Bayesian MSM very slow

4

Hi, Im trying to follow the tutorial 6 (http://emma-project.org/latest/tutorials/notebooks/06-expectations-and-observables.html#Dynamic/kinetic-experimental-observables) to calculate the Trp-flourescene auto-correlation. When I run this code ``` %matplotlib inline import matplotlib.pyplot as plt import matplotlib as mpl...

H-EKE

Bayesian Hidden Markov model got an unexpected keyword argument 'desc'

1

When I want to analyze Hidden Markov Network, I have the following problem `hmm=pyemma.msm.bayesian_hidden_markov_model(dtrajs,5, lag=30,stride=10, mincount_connectivity=0.2)` > Sampling HMSMs: 0%| | 0/100 [00:00

ShenWenHuibit

i am following the tutorial on the pyEMMA website on my system and when i calculate the fraction of used states and counts they appear as 0.38 and 0.48, respectively....

hima111997

in notebook 07, this line : `hmm_4 = pyemma.msm.bayesian_hidden_markov_model(cluster.dtrajs, nstates=4, lag=1, dt_traj='1 ps', nsamples=50) ` produces this error: ``` --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[5], line 1...

hima111997

i have 21 metastable states and when trying to use pyemma.plots.plot_cktest the subplots are very small and i cant see anything. Is there a way to increase the size of...

hima111997

Is it possible to use pyemma.msm.its on the dtrajs after using TICA on the features? ``` def sample_k_centers_after_tica(n, data): cl_original = pyemma.coordinates.cluster_kmeans(data= data, k=n, stride=1, max_iter=40) its = pyemma.msm.its(cl_original.dtrajs, lags=[1,...

hima111997

Here's a quick checklist in what to include: when i use add_sidechain_torsions it produces an error: ``` TypeError Traceback (most recent call last) Cell In[62], line 8 5 xtc =...

hima111997

- [ ] Include a detailed description of the bug or suggestion: i am watching this video https://youtu.be/zvgYjfQ9Vb8?list=PLych0HcnzSQIBl_AZN5L2cMZvOfyhzjd8&t=469 and trying to apply the code on my trajectory. in the part...

hima111997

**Dear Experts, I have carried out MSM using pyemma, taking different order parameters as input. I have been able to obtain distinct macrostates. I have extracted 100 structures from the...

dulalmondal123

Dear Users, I am new to PyEMMA. I want to use two features, one as the CA distance between two proteins and the tilt angles between two proteins. How to...

Chakrabort123