Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

Cheng Zhang, Chun Liang Lai, Bernard Pettitt

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The weighted histogram analysis method (WHAM) for free energy calculations is a valuable tool to produce free energy differences with the minimal errors. Given multiple simulations, WHAM obtains from the distribution overlaps the optimal statistical estimator of the density of states, from which the free energy differences can be computed. The WHAM equations are often solved by an iterative procedure. In this work, we use a well-known linear algebra algorithm which allows for more rapid convergence to the solution. We find that the computational complexity of the iterative solution to WHAM, and the closely-related multiple Bennett acceptance ratio method can be improved using the method of direct inversion in the iterative subspace. We give examples from a lattice model, a simple liquid and an aqueous protein solution.

Original languageEnglish (US)
Pages (from-to)1079-1089
Number of pages11
JournalMolecular Simulation
Volume42
Issue number13
DOIs
StatePublished - Sep 1 2016

Fingerprint

histograms
Histogram
Free energy
Inversion
Subspace
inversions
free energy
Free Energy
Linear algebra
iterative solution
Computational complexity
estimators
acceptability
Proteins
algebra
Liquids
Iterative Solution
Density of States
Iterative Procedure
Lattice Model

Keywords

  • DIIS
  • Free energy
  • MBAR
  • WHAM

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Modeling and Simulation
  • Chemistry(all)
  • Chemical Engineering(all)
  • Materials Science(all)
  • Information Systems

Cite this

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace. / Zhang, Cheng; Lai, Chun Liang; Pettitt, Bernard.

In: Molecular Simulation, Vol. 42, No. 13, 01.09.2016, p. 1079-1089.

Research output: Contribution to journalArticle

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