𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Multidimensional free-energy calculations using the weighted histogram analysis method

✍ Scribed by Shankar Kumar; John M. Rosenberg; Djamal Bouzida; Robert H. Swendsen; Peter A. Kollman

Publisher
John Wiley and Sons
Year
1995
Tongue
English
Weight
824 KB
Volume
16
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

The recently formulated weighted histogram analysis method (WHAM)' is an extension of Ferrenberg and Swendsen's multiple histogram technique for freeenergy and potential of mean force calculations. As an illustration of the method, we have calculated the two-dimensional potential of mean force surface of the dihedrals gamma and chi in deoxyadenosine with Monte Carlo simulations using the all-atom and united-atom representation of the AMBER force fields. This also demonstrates one of the major advantages of WHAM over umbrella sampling techniques. The method also provides an analysis of the statistical accuracy of the potential of mean force as well as a guide to the most efficient use of additional simulations to minimize errors.

πŸ“œ SIMILAR VOLUMES

Convergence and error estimation in free
Convergence and error estimation in free energy calculations using the weighted histogram analysis method
✍ Fangqiang Zhu; Gerhard Hummer πŸ“‚ Article πŸ“… 2011 πŸ› John Wiley and Sons 🌐 English βš– 906 KB

## Abstract The weighted histogram analysis method (WHAM) has become the standard technique for the analysis of umbrella sampling simulations. In this article, we address the challenges (1) of obtaining fast and accurate solutions of the coupled nonlinear WHAM equations, (2) of quantifying the stat

Monte Carlo study of ligand–protein bind
Monte Carlo study of ligand–protein binding energy landscapes with the weighted histogram analysis method
✍ Djamal Bouzida; Paul A. Rejto; Gennady M. Verkhivker πŸ“‚ Article πŸ“… 1999 πŸ› John Wiley and Sons 🌐 English βš– 235 KB πŸ‘ 2 views

The thermodynamics of molecular recognition is investigated by a statistical energy landscape approach, where the temperature profile of the ligand᎐protein binding process is determined using the weighted histogram analysis method. The analysis reveals differences in the binding energy landscapes of

Improving the efficiency and reliability
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
✍ Nandou Lu; David A. Kofke; Thomas B. Woolf πŸ“‚ Article πŸ“… 2003 πŸ› John Wiley and Sons 🌐 English βš– 166 KB

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-ener