✦ LIBER ✦

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

✍ Scribed by Michael S. Lee; Freddie R. Salsbury Jr.; Mark A. Olson

Publisher: John Wiley and Sons
Year: 2004
Tongue: English
Weight: 307 KB
Volume: 25
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.20119

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald (PME) method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1967–1978, 2004

📜 SIMILAR VOLUMES

An efficient method for solving implicit

An efficient method for solving implicit and explicit stiff differential equations

✍ H. Pasic 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 195 KB 👁 2 views

When the s-stage fully implicit Runge}Kutta (RK) method is used to solve a system of n ordinary di!erential equations (ODE) the resulting algebraic system has a dimension ns. Its solution by Gauss elimination is expensive and requires 2sn/3 operations. In this paper we present an e$cient algorithm,

An efficient explicit/implicit domain de

An efficient explicit/implicit domain decomposition method for convection-diffusion equations

✍ Liyong Zhu; Guangwei Yuan; Qiang Du 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 308 KB

Discrimination between native and intent

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model

✍ Yury N. Vorobjev; Juan Carlos Almagro; Jan Hermans 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 179 KB 👁 3 views

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational