Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here, we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically, we have implemented this new approach within the more computationally efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the lambda end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality is planned to be included in the next major release of Amber (scheduled for release in Q1 2014), available at http://ambermd.org, under the Amber license.