FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post–processing methods like MM–PBSA and LIE.  FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine.  The latest releases are available from the project web page.  A 32bit Linux virtual machine image with FESetup pre–installed is available here (see README.txt in the zip archive for user name and password).

Other Software:

ProtoMS - a complete protein Monte Carlo free energy simulation package.

Sire - a complete python/C++ molecular simulation framework, particularly focussed around Monte Carlo, QM/MM and free energy methods.

PCAZIP - a toolkit for compression and analysis of molecular dynamics trajectories.

COCO - a tool to enrich an ensemble of structures, obtained e.g. from NMR.

Handy Routines for Ptraj/Cpptraj - additional analysis methods for ptraj and cpptraj.