Tutorials

Here you can find a list of available tutorials that provide input files and a step-by-step guide on how to perform alchemical free energy calculations using pmx for a few typical use cases:

• Protein mutation
• Ligand mutation
• DNA/RNA mutation
• Large-scale scans
• Analysis

Before getting straight into the simulations, we would suggest to familiarise yourself with the concepts at the foundation of this type of calculations as well as with how pmx works. In this regard, here we provide a few useful references:

1. 22. Gapsys, S. Michielssens, D. Seeliger, B.L. de Groot; pmx: Automated protein structure and topology generation for alchemical perturbations; J. Comp. Chem. 2014, 36(5), 348–354

2. 22. Gapsys, S. Michielssens, J.H. Peters, B.L. de Groot, H. Leonov; Calculation of binding free energies; Method Mol. Biol 2015, vol. 1215, Humana Press

3. 13. Aldeghi, B.L. de Groot, V. Gapsys; Accurate calculation of free energy changes upon amino acid mutation; Method Mol. Biol 2018, vol. XXXX, Humana Press