On the calculation of entropy from covariance matrices of the atomic fluctuations

被引:456
作者
Andricioaei, I
Karplus, M [1 ]
机构
[1] Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
[2] Univ Strasbourg, Inst Le Bel, F-67070 Strasbourg, France
关键词
D O I
10.1063/1.1401821
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
An ad hoc method for calculating the entropy of a biomolecular system from the covariance matrix of the atomic fluctuations is analyzed. It is shown that its essential assumption can be eliminated by a quasiharmonic analysis. The computer time required for use of the latter is of the same order as that of the former. (C) 2001 American Institute of Physics.
引用
收藏
页码:6289 / 6292
页数:4
相关论文
共 20 条
[1]   Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation [J].
Bernstein, BE ;
Michels, PAM ;
Hol, WGJ .
NATURE, 1997, 385 (6613) :275-278
[2]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[3]   HARMONIC-ANALYSIS OF LARGE SYSTEMS .1. METHODOLOGY [J].
BROOKS, BR ;
JANEZIC, D ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (12) :1522-1542
[4]  
Chaires JB, 1997, BIOPOLYMERS, V44, P201, DOI 10.1002/(SICI)1097-0282(1997)44:3<201::AID-BIP2>3.0.CO
[5]  
2-Z
[6]   Thermodynamic analysis of biomolecular interactions [J].
Cooper, A .
CURRENT OPINION IN CHEMICAL BIOLOGY, 1999, 3 (05) :557-563
[7]   FREE-ENERGY DETERMINATION OF POLYPEPTIDE CONFORMATIONS GENERATED BY MOLECULAR-DYNAMICS [J].
DINOLA, A ;
BERENDSEN, HJC ;
EDHOLM, O .
MACROMOLECULES, 1984, 17 (10) :2044-2050
[8]   ENTROPY ESTIMATION FROM SIMULATIONS OF NON-DIFFUSIVE SYSTEMS [J].
EDHOLM, O ;
BERENDSEN, HJC .
MOLECULAR PHYSICS, 1984, 51 (04) :1011-1028
[9]   AN OPTIMIZED HARMONIC REFERENCE SYSTEM FOR THE EVALUATION OF DISCRETIZED PATH-INTEGRALS [J].
FRIESNER, RA ;
LEVY, RM .
JOURNAL OF CHEMICAL PHYSICS, 1984, 80 (09) :4488-4495
[10]   SIMULATION ANALYSIS OF TRIOSE PHOSPHATE ISOMERASE - CONFORMATIONAL TRANSITION AND CATALYSIS [J].
KARPLUS, M ;
EVANSECK, JD ;
JOSEPH, D ;
BASH, PA ;
FIELD, MJ .
FARADAY DISCUSSIONS, 1992, 93 :239-248