Fast ABFE

Investigating rapid ABFE calculations with A3FE.

To Run Example

Install A3FE and dependencies
Clone this repo with git clone https://github.com/michellab/fast_abfe.git
Edit the slurm script at master_input/run_somd.sh to run with your slurm installation (change the partition etc)
Enter desired directory, e.g. cd cyclod
Run python ../master_input/run_all_a3fe.py (currently set to run 0.1 ns / window simulations)

To Analyse

See analysis.py in the scripts directory for examples of analyses you could perform.

To Run New Sets of Simulations

Assuming the system is part of https://github.com/openforcefield/protein-ligand-benchmark:

Pull the benchmark_repo into this directory
See scripts/setup_pl_benchmark_inp.py for an automated setup procedure. Run this.
Attempt to run the full set as above with run_all_a3fe.py
You are likely to run into issues parameterising the protein. If this is the case, see the tip here for help.