✦ LIBER ✦

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

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

Publisher: John Wiley and Sons
Year: 1992
Tongue: English
Weight: 965 KB
Volume: 13
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.540130812

No coin nor oath required. For personal study only.

📜 SIMILAR VOLUMES

Multidimensional free-energy calculation

Multidimensional free-energy calculations using the weighted histogram analysis method

✍ Shankar Kumar; John M. Rosenberg; Djamal Bouzida; Robert H. Swendsen; Peter A. K 📂 Article 📅 1995 🏛 John Wiley and Sons 🌐 English ⚖ 824 KB

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 surfa

Convergence and error estimation in free

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

✍ Fangqiang Zhu; Gerhard Hummer 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 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 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 235 KB 👁 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

On suitable formulations of the method o

On suitable formulations of the method of modal analysis for numerical calculations

✍ E. Gobmann; W. Krings; H. Waller 📂 Article 📅 1978 🏛 John Wiley and Sons 🌐 English ⚖ 424 KB

The method of modal analysis is a method widely used in structural analysis of linear systems. After a short introduction two step by step formulations for modal calculations are discussed. One of them is of more theoretical interest, the other is recommended for practical calculations for multi-deg

On the Surface Free Energy of PVC/EVA Po

On the Surface Free Energy of PVC/EVA Polymer Blends: Comparison of Different Calculation Methods

✍ Marie-Caroline Michalski; Joël Hardy; Benilde J.V. Saramago 📂 Article 📅 1998 🏛 Elsevier Science 🌐 English ⚖ 186 KB

The surface free energy of polymeric films of polyvinylchloride (PVC) + poly(ethylene-co-vinylacetate) (EVA) blends was calculated using the van Oss treatment (Lifshitz and electron donor-electron acceptor components of surface free energy) and the Owens-Wendt treatment (dispersive and nondispersive

Methods for calculating the absolute ent

Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics

✍ Hagai Meirovitch 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 655 KB

## Abstract The commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations __i__ correctly with the Boltzmann probability, __P__, while the __value__ of __P__ is not provided directly; theref