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vvoelz / biceps

Bayesian inference of conformational populations
https://github.com/vvoelz/biceps
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MBAR version #8

Closed yunhuige closed 6 years ago

yunhuige commented 7 years ago

The current scripts only works well with pymbar 2.1.0b0 version and don't work with pymbar 3.0 (tested)! We may have to fix it or specify MBAR version for users.

yunhuige commented 6 years ago

I think I fixed this bug but I need to do more tests.

yunhuige commented 6 years ago

Updated: I did tests using 2 different versions Pymbar (2.1.0 vs 3.0.3) and here is what I found: our old scripts for this line is this: (Deltaf_ij, dDeltaf_ij) = mbar.getFreeEnergyDifferences() It works well with v2.1.0 but doesn't work with v3.0.3. To fix it, we need replace it with either of the following lines: (Deltaf_ij, dDeltaf_ij, Theta_ij) = mbar.getFreeEnergyDifferences(uncertainty_method='svd-ew') or (Deltaf_ij, dDeltaf_ij, Theta_ij) = mbar.getFreeEnergyDifferences(uncertainty_method='approximate') But I found either of these lines doesn't work with v2.1.0. So here is my suggestion: in the future we use the later MBAR scripts and we also ask people to use that version. We are going to abandon the old scripts and Pymbar v2.1.0.