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markovmodel / pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA
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Issues on MSM estimation and validation in Notebook 00 #200

Open Owen2015 opened 1 year ago

Owen2015 commented 1 year ago

When I ran the code block

its = pyemma.msm.its(cluster.dtrajs, lags=50, nits=10, errors='bayes') pyemma.plots.plot_implied_timescales(its, units='ns', dt=0.1);

It show "estimating BayesianMSM: 80%" and I ran it multiple times but it just fluctuated between 50%-90% and never reach 100%.

Can anyone help on this?

bsayari10 commented 11 months ago

Try this: its = pyemma.msm.its(cluster.dtrajs, lags=50, nits=6, errors="bayes" , n_jobs = 1) pyemma.plots.plot_implied_timescales(its, units='ns', dt=0.1);

n_jobs is ambiguous in this case. Hope this helps.