04_fep

Alchemical free energy Tutorials

Requirements:

• BioSimSpace
• GROMACS

1. Intro to Alchemistry

Authors:

• Antonia Mey -- @ppxasjsm
• Lester Hedges -- @lohedges
• Finlay Clark -- @fjclark
• Anna Herz -- @annamherz

An introduction to the basics of running alchemical free energy calculations in BioSimSpace, including loading and parameterising systems, morphing ligands, running solvation and binding free energy calculations, and analysis.

2. Relative Binding Free Energy Calculations

Authors:

• Jenke Scheen -- @jenkescheen
• Anna Herz -- @annamherz

An overview for setting up, running, and analysing a perturbation network for alchemical relative binding free energies. This includes a setup and analysis notebook, along with sample scripts for running on a slurm cluster.

03. Absolute Binding Free Energy Calculations

Authors:

• Finlay Clark -- @fjclark

Functionality for running alchemical absolute binding free energy calculations is currently present in the Exscientia Sandpit within BioSimSpace. These notebooks discuss the idea of Sandpits for including experimental features in BioSimSpace, and detail setting up and analysing absolute binding free energy calculations.

03. Protein Free Energy Calculations

Authors:

• Audrius Kalpokas -- @akalpokas

An introduction to alchemical protein free energy calculations. Specifically, this includes an overview of BioSimSpace region-of-interest (ROI) functionality and examples of how to setup, view and export alchemical protein systems.

05. Alchemical Transfer RBFE Calculations

Authors:

• Matthew Burman -- @mb2055

An overview of alchemical transfer functionality within BioSimSpace. Includes methods for setting up ATM-compatible systems, as well as custom protocols for minimisation, equilibration and production.