Paper Citing NAMD - Abstract
Holland, Bryan W.; Vafaei, Shaghayegh; Tomberli, Bruno
Computer data analysis of the oscillating forward-reverse method
JOURNAL OF COMPUTATIONAL PHYSICS, 231:4355-4364, JUN 1 2012
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 5 GB) 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. (C) 2012 Elsevier Inc. All rights reserved.
