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choderalab / AURKA_UMN

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Add script to compute water normalized fluctuation correlation functions #35

Closed jchodera closed 8 years ago

jchodera commented 8 years ago

This adds a script to compute normalized fluctuation correlation functions for the W1 and W2 sites.

I'll add a function to also compute the integrated autocorrelation time momentarily.

jchodera commented 8 years ago

The correlation.py library needs to be cleaned up---this was a quick edit of the pymbar.timeseries library.

The main figure can be seen here. This will need to be cleaned up too. We'll probably want to show W1 and W2 correlation functions +/- TPX.

jchodera commented 8 years ago

@juliebehr : Can you check that I got the -TPX (1OL5?) and +TPX (1OL7?) identities right in the analyze-hbond-correlation-times.py script?

jchodera commented 8 years ago

This is probably good enough for now. I can add bootstrapped error bars later.