Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems

被引:110
作者
Patel, Sandeep [1 ]
Brooks, Charles L., III [1 ]
机构
[1] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA
基金
美国国家科学基金会;
关键词
polarizable force field; biomolecules; fluctuating charge; charge equilibration; CHARMM;
D O I
10.1080/08927020600726708
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The past decade has seen intense development of what are anticipated to be the next generation of classical force fields to be used in computational statistical mechanical approaches to studying a broad class of physical and biological systems. Among the several approaches being actively pursued currently is the fluctuating charge (or equivalently charge equilibration or electronegativity equalization) method. Within this formalism, dynamical electronic degrees of freedom are introduced and propagated in time in order to allow an electrostatic response to the local chemical environment. In this article, we present a review of our recent development and application efforts of a polarizable biomolecular force field based on the fluctuating charge formalism and founded on the CHARMM non-polarizable force field. We will discuss aspects of the parameterization, as well as recent applications to a spectrum of chemical and biological systems such as small-molecule liquid-vapor interfaces, solvated proteins/peptides, and physiological membrane systems. We will conclude with brief comments on aspects that require continued effort in terms of future development of such novel potentials.
引用
收藏
页码:231 / 249
页数:19
相关论文
共 113 条
[1]  
Allen M. P., 2009, Computer Simulation of Liquids
[2]   Energetics of ion conduction through the gramicidin channel [J].
Allen, TW ;
Andersen, OS ;
Roux, B .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (01) :117-122
[3]   MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE [J].
ANDERSEN, HC .
JOURNAL OF CHEMICAL PHYSICS, 1980, 72 (04) :2384-2393
[4]   Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator [J].
Anisimov, VM ;
Lamoureux, G ;
Vorobyov, IV ;
Huang, N ;
Roux, B ;
MacKerell, AD .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2005, 1 (01) :153-168
[5]  
[Anonymous], J PHYS CHEM REF DA S
[6]  
[Anonymous], 1976, CHEM BONDS BONDS ENE
[7]   Parametrizing a polarizable force field from ab initio data.: I.: The fluctuating point charge model [J].
Banks, JL ;
Kaminski, GA ;
Zhou, RH ;
Mainz, DT ;
Berne, BJ ;
Friesner, RA .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (02) :741-754
[8]   The structure of liquid ethanol: A neutron diffraction and molecular dynamics study [J].
Benmore, CJ ;
Loh, YL .
JOURNAL OF CHEMICAL PHYSICS, 2000, 112 (13) :5877-5883
[9]   Molecular dynamics of the KcsA K+ channel in a bilayer membrane [J].
Bernèche, S ;
Roux, B .
BIOPHYSICAL JOURNAL, 2000, 78 (06) :2900-2917
[10]   Second-generation wave-function thermostat for ab initio molecular dynamics -: art. no. 104303 [J].
Blöchl, PE .
PHYSICAL REVIEW B, 2002, 65 (10) :1-9