I discuss a number of molecular simulationtechniques recently included in the GROMACS molecular dynamics package for calculatingfree energy differences between two user-defined end states. These include Hamiltonian replica exchange with all-to-all state swaps and the capability to perform expanded ensemble simulations.
We also discuss the validation efforts used to check the implementation of these free energy calculation methods in GROMACS, and show how these methods canbe usedto very finely test the sensitivity of calculated free energies to different methods for performing long range force cutoffs and or other types of simulation approximations.
I also address a number of other recent additions to GROMACS, such as GPU computing capabilities and PME-based long-range dispersion calculations.
