Free Energy Tools

More tools will be posted at some point in the future, as many are in development. Here's what we've got so far:

• File:Amb2gmx.gz: A perl script to convert AMBER topologies and coordinates into GROMACS topologies and coordinates. It requires an AMBER installation (tested with AMBER 8 and AMBER 9). We have frequently used it for converting small molecule topologies and coordinates generated using ANTECHAMBER to GROMACS format, although in principle it should work for larger systems as well. Please report any bugs that are found to dmobley - at - gmail.com. No known bugs. To give credit where credit is due, this is a tool we updated and extended from one originally written by E. Sorin in the Pande group. If you use this script for a publication, you should reference D. L. Mobley, J. D. Chodera, K. A. Dill. "On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations", Journal of Chemical Physics 125:084902, 2006.

• A Python module (based on numpy) for estimating free energy differences and equilibrium expectations from multiple equilibrium simulations of different thermodynamic states. Downloadable from [SimTK]. The estimator employed is similar to WHAM but is derived without histograms, and uncertainty estimates are available. This can be used to analyze alchemical free energy calculations, umbrella sampling simulations, or generalized-ensemble simulations (such as simulated or parallel tempering). The estimator is described the publication: M. R. Shirts and J. D. Chodera. Statistically optimal analysis of multiple equilibrium simulations. J. Chem. Phys, 129:124105 (2008) [1]