How to create input without using a parser?

[9527567]

In this issue, with @egallicc's help, using pymbar to analyze the binding energy of AToM-OpenMM has become a reality. I tried to read and understand the tutorial, but unfortunately I am not an expert in statistics.

[orbeckst]

I converted your issue to a discussion because it's not an issue in the library but a question.

If you already have data in a form suitable for pymbar then you might not need alchemlyb.

If you want to use alchemlyb then you have to bring your data into the standard form of raw data as described in the docs; the u_nk standard form seems to be most relevant to you, given that you want to use MBAR. Once you have a pandas data frame with the correct information, you can use alchemlyb's subsampler, estimator, and visualization modules.

[xiki-tempula]

If you have the reduced potential as a numpy array. I have this old script that might help you.
#296 (reply in thread)

[9527567]

thank you.