Closed buruiyu closed 2 years ago
Hey, sample by state does not use any weighting, the structures are drawn uniformly from the pool of frames that are assigned to the particular state. If they deviate a lot, it could mean that either your projection isn't good or the clustering doesn't use enough centers (# cluster centers == # states).
Cheers!
Hello! I am a new learner. I am using pyemma on linux system. My pyemma version is 2.5.11. After I constructed the model, I found that the representative structures saved inside each macrostate were different, so I first used
print(msm.metastable_distributions[1])
to get the distribution of a macrostate over each microstate, and selected the microstate with the highest probability; then usedmsm.sample_by_state( 10 , [1])
to extract 10 structure from inside a microstate, and then usepyemma.coordinates.save_trajs
to save it. I extracted 10 structures from inside each microstate usingsample_by_state
, what is the criteria for extracting structures with this line of code? Is each structure extracted sorted by some weight? After I extracted it this way, the gap between each structure inside the microstates is still large, so I want to extract some structures near the cluster centroid of the microstates, how should I implement it?Thank you!