Computer data analysis of the oscillating forward-reverse method

  • Authors:

  • Bryan W. Holland;Shaghayegh Vafaei;Bruno Tomberli

  • Affiliations:

  • Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1;Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1;Department of Physics and Astronomy, Brandon University, Brandon, Manitoba, Canada R7A 6A9

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2012

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Abstract

Nonequilibrium work theorems have recently gained wide acceptance as useful tools in determining free energy profiles for soft-matter systems. We have recently proposed an extension of the forward-reverse method, called the oscillating forward-reverse method; by introducing an oscillatory drift it enables the user to obtain PMFs from a single nonequilibrium pull. The analysis, although manageable, is non-trivial. We present here the data analysis and the software (OFR-AT) created to construct PMFs and associated uncertainties from the oscillating forward-reverse (OFR) method. The output analyzed by OFR-AT is often from molecular dynamics simulations, but as with the OFR method itself, it can be more generally applied. OFR-AT is a fast and efficient analysis tool that can analyze very large files (larger than 5GB) in a short time period. We also describe the uncertainty and correlation calculations performed, provide a map of the data flow through the program, and present representative examples of PMF profiles calculated using OFR-AT.