Kyle Beauchamp

I'm happy closing until later. We might be reworking the app / scripts for MSMB3 anyway.

Use MDTraj to load Gens.lh5 and calculate pairwise RMSD: http://mdtraj.org/latest/examples/clustering.html

Oops, I misread your question. You'll also have to find the centroids of each each state. That also could be done, but it's not automated so you'll have to write...

Or you could do something like drawing random samples from each macrostate, then, calculating RMSDs between the drawn samples.

I don't think we have that function written. On Tue, May 20, 2014 at 5:14 PM, Wei Dai [email protected] wrote: > I prefer the centroid structures. Could you tell me...

Nice find!

OK I guess what happened was that Robert split the tICA doc into theory and application but never ported the application side of things. I wonder if it makes more...

Do you have a preferred way to generate the atom pairs? Otherwise, I vote that we include a tiny script inside the tutorial (probably at the very end, in a...

Also, I wonder if it might make sense to set stride = 1 for the "beginner" TICA tutorial. Otherwise there's just a lot of parameters exposed to users. I know...

Also: the "Drawbacks of TICA" section actually applies to _all_ MSM-like forms of dimensionality reduction, so it might not be necessary.