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michellab / a3fe

Automated Adaptive Absolute alchemical Free Energy calculator
https://a3fe.readthedocs.io/en/latest
GNU General Public License v3.0
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Separated Topologies method #3

Open nffaruk opened 2 months ago

nffaruk commented 2 months ago

Hi, nice work on the package! As you note in your paper, computational resource limits can get in the way of practicality. I was wondering if you considered the Seperated Topologies method here: https://pubs.acs.org/doi/10.1021/acs.jctc.3c00282 How difficult would it be to support such a scheme within a3fe and if you have pointers on which source files to look at to modify. Their repo: https://github.com/MobleyLab/SeparatedTopologies

fjclark commented 1 month ago

Hi, thanks! And thanks for the question/ suggestion. It's an exciting approach and I'd like to play around with it. The best way to implement this in a3fe would likely be:

  1. Modify BioSimSpace to allow setup of SepTop calculations in GROMACS (as a3fe relies on BioSimSpace for all setup)
  2. Update a3fe to handle GROMACS output files

I don't think 2. should be too hard, and I'm hoping to get round to it in a few months to allow ABFE with GROMACS. Unfortunately, 1. might require more time than I'll have before I finish my PhD (early next year), although I'll have a closer look at the Mobley Lab repo you sent.

nffaruk commented 1 month ago

Thanks for the response. I've found out that OpenFE is in the process of incorporating SepTop, so then it may not be worth it considering your time crunch till graduation.

fjclark commented 1 month ago

Great, that's exciting. Yes, in that case I won't put time into this soon, but I'll keep the issue open as an enhancement request for future. Thanks.

lohedges commented 1 month ago

There is also femto, which supports both AToM and SepTop via OpenMM. This can be used as a standalone library, or via the command-line. (It also has support for running using repex and analysis.)

nffaruk commented 1 month ago

Thanks for pointing to femto, will check it out! But from a glance, a3fe seems a lot more streamlined than it - will be cool if the enhancement ever comes to fruition.