Part 7 - Merged Molecules and Lambda Levers#

In the last chapter we learned how to use sire to set up and run alchemical free energy calculations. We saw how the concept of a merged molecule, together with a lambda lever, enabled us to define a perturbation between two end states, and then run a set of OpenMM GPU-accelerated molecular dynamics simulations to calculate the free energy between those states.

In this chapter we will dive deeper into the machinery of sire that supports the creation and management of merged molecules. We will see how this, plus more advanced use of lambda levers enables the running of more complex free energy simulations. These include those to calculate absolute binding free energies, calculate free energies of perturbing individual residues in proteins, and calculating free energies that involve breaking rings in ligands.