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Added 'autotune' command for automated tuning of alchemical protocol

See original GitHub issue

We should add an autotune command to the cli that would attempt to optimize the alchemical protocol to minimize the discrete analog to thermodynamic length by reweighting existing data in the repex stores.

Issue Analytics

State:
Created 9 years ago
Comments:7 (7 by maintainers)

Top GitHub Comments

1reaction

jchoderacommented, Jul 18, 2017

I think there should be two distinct features:

(1) Construct an initial guess for the alchemical protocol (implemented for yank 1.0)
(2) Update the alchemical protocol based on an existing simulation (implemented sometime in the future)

For (1), I like the idea of adding the auto keyword directly to the protocol description in the YAML. Is it possible that, as YANK generates the explicitly substituted YAML file for the experiment it is about to run, it could detect whether auto is used and carry out the fast lambda scan to produce an initial protocol guess at that point, and then fill in the explicit protocol in the experiment directory? Or would this make early termination unrecoverable?

0reactions

Lnadencommented, Aug 21, 2017

Fixed in #726

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