Executing RBFE and ABFE on Local Workstation

[Dslab2025]

I want to set up RBFE (Relative Binding Free Energy) and ABFE (Absolute Binding Free Energy) simulations on my local workstation. How can I run them? The tutorial provides a SLURM shell script, but it is not working.

Our workstation is equipped with a 32-core CPU, two NVIDIA RTX 4080 GPUs, and runs on Linux Mint OS. GROMACS 2024 and Amber (with pmemd.cuda) are installed and declared in the ~/.bashrc file.

[jmichel80]

Verify in the first instance that your local slurm setup is working.

The slurm scripts we provide have to be modified to use your local queue settings.

If you have established slurm works for you for other types of calculations but you still struggle with the tutorial scripts post more info about the error messages you see.

[fjclark]

Hi @Dslab2025, for the ABFE only, you might find it easier to use https://github.com/michellab/a3fe (and documentation). This uses BioSimSpace behind the scenes but automates the SLURM submission.

[Dslab2025]

@fjclark shall it execute that tool on my Linuxmint Workstation (Not PC)? I dont have SLURM

[jmichel80]

@Dslab2025 - you need to have a working installation of slurm first. You also need to be sufficiently familiar with slurm to know how to adapt the provided slurm scripts to your local queue settings.

[Dslab2025]

ok