Computer data analysis of the oscillating forward–reverse method
Journal of Computational Physics(2012)
摘要
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.
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关键词
Nonequilibrium,PMF,Oscillating forward–reverse,Molecular dynamics
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