Part 6 - Morphs and Alchemical Free Energies#
One of the original design goals of sire was to support the
prototyping, setup and running of alchemical free energy simulations.
sire has a lot of in-built support for perturbing (morphing)
between different molecules, and to simulate and then calculate
alchemical free energy differences along those morphs.
This is supported by integration with OpenMM, thereby letting you set up and run molecular dynamics simulations that morph one molecular system into another.
This chapter will teach you how to set up a morph, how to run alchemical molecular dynamics simulations, and how to calculate alchemical free energies along morph coordinates. This includes how to add restraints to atoms, fix atoms in space, and change these restraints as you perturb between different molecules.