search

OpenBioSim / biosimspace_tutorials

A tutorials suite for BioSimSpace.
GNU General Public License v3.0
14 stars 5 forks source link

Tutorial 4: 01_setup_rbfe - update required for amber support #8

Open jmichel80 opened 1 year ago

jmichel80 commented 1 year ago

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 commented 1 year ago

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 commented 2 months ago

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

lohedges commented 2 months ago

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 commented 2 months ago

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

lohedges commented 1 month ago

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.