Tutorial 4: 01_setup_rbfe - update required for amber support

[jmichel80]

If we want to report support for AMBER FEP in this tutorial we will need to merge in devel the functionality currently in https://github.com/michellab/BioSimSpace/tree/feature-amber-fep

[lohedges]

This is on my to-do list. However, there have been quite a few changes in the Exs fork so I'll need to wait until I synchronize to avoid needing to do things twice. It also requires the analysis code, which is still based on Michellab and needs refactoring.

[vwcruzeiro]

Hello @jmichel80 and @lohedges . Is there an example on how to run the code using AMBER FEP? Thank you!

[lohedges]

Hello there,

The AMBER FEP code is now in core BioSimSpace. I am actually in the process of updating the tutorial and testing. I'm hoping this will be done within the next couple of weeks.

I'll update this thread when I'm finished.

[vwcruzeiro]

Great! Thank you for your reply @lohedges . Looking forward to giving it a try. All the best.

[lohedges]

Hi there. Just to say that I'm working on this here. I'd like to test this end-to-end with a simple example before raising a PR. I also need to update the installation instructions in the top-level README file, i.e. update the versions for the various requirements. Currently the provided SLURM script uses pmemd.cuda only. I can add an option to set the exe name via the environment if needed, e.g. something like AMBER_EXE. That way it would be easy to use the script with pmemd or pmemd.cuda, or whatever name is used locally.

[architecttherapeutics]

Hello @lohedges ! Is there an example or tutorial I could follow so I can give this a try? Looking forward to that! Thank you

[lohedges]

Hi there,

You should just be able to follow the existing RBFE tutorial using this feature branch rather than main. It is currently being tested internally, so there may be adjustments to the tutorial in the near future. Alternatively, you could just follow the tutorial here, which shows how AMBER can be used as an engine for FEP simulations. (In this case, hydration free energy calculations.)

Cheers.