Implementations of nonequilibrium methods for free energy calculations: forthcoming developments of the ORAC molecular dynamics simulation code

Abstract

ORAC is a FORTRAN suite to simulate complex biosystems at the atomistic level. The program’s engine is supplemented by multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature algorithms. Quite recently, several advanced techniques for enhanced sampling in atomistic systems have been implemented, including replica exchange with solute tempering, metadynamics, steered molecular dynamics, serial generalized ensemble simulations and nonequilibrium alchemical transformations. All these computational technologies have been devised for parallel architectures using the standard MPI communication protocol. [...]