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

ABSTRACT: 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 computational 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 functionalit

SUBMITTER: Kaus JW 

PROVIDER: S-EPMC3811123 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature