jmichel80
commented
1 year ago Hi,
Currently the API doesn't support setup of non-equilibrium FEP calculations and there isn't support for a generic HREX interface but it is possible with a little bit of work to setup inputs with BSS, run HREX simulations with a chosen engine outside of the framework and load back the trajectories for analysis.
We are currently consolidating various branches that implement different flavours of FEP using different engines. At the moment it is probably difficult to develop this part of the codebase without prior knowledge. Most of the changes required would be in https://github.com/michellab/BioSimSpace/tree/devel/python/BioSimSpace/FreeEnergy and https://github.com/michellab/BioSimSpace/tree/devel/python/BioSimSpace/Process
Julien
noahharrison64
Hi,
I just discovered this repo and look forward to having a play around with BioSimSpace. I was hoping to conduct some non-eq FEP calculations such as those detailed in this paper. I wonder whether this will be possible using your API. It's my understanding that during the production stage, there needs to be functionality to change lambda values over the course of the short transition simulations between state A and state B. And then during the analysis stage implementations of the Crooks fluctuation and Jarzynski theorems are required.
I'd also be interested in eventually attempting to implement Hamiltonian Replica Exchange (HREX) as a method for eq-FEP.
Are there any considerations for making these non-canonical FEP protocols easily implemented in BioSimSpace? Or would anyone have any pointers for how to go about implementing such protocols with existing architecture?
Thanks, Noah