Absolute entropies from molecular dynamics simulation trajectories

被引：164

作者：

Schäfer, H ^{[1
]}

Mark, AE ^{[1
]}

van Gunsteren, WF ^{[1
]}

机构：

[1] ETH Zentrum, Swiss Fed Inst Technol, Phys Chem Lab, CH-8092 Zurich, Switzerland

来源：

JOURNAL OF CHEMICAL PHYSICS | 2000年 / 113卷 / 18期

关键词：

D O I：

10.1063/1.1309534

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：

A heuristic formula for calculating absolute entropies from the covariance matrix of atom-positional fluctuations was extensively tested. Because of its heuristic nature, the results obtained are compared to analytical expressions for an ensemble of harmonic oscillators, for the ideal gas, and to numerical results obtained from the equation of state for the Lennard-Jones fluid as a means of validation of the approximate formula for the entropy. The formula yields rather accurate results. The removal of translational and rotational rigid body motion and the effect of the various fitting procedures involved are discussed for the more realistic system of a beta -heptapeptide in solution. (C) 2000 American Institute of Physics. [S0021-9606(00)51539-6].

引用

页码：7809 / 7817

页数：9

共 14 条

[1]

Allen M. P., 1989, COMPUTER SIMULATION

[2]

Daura X, 1999, PROTEINS, V34, P269, DOI 10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO

[3]

2-3

[4] Reversible peptide folding in solution by molecular dynamics simulation [J].

Daura, X ;

Jaun, B ;

Seebach, D ;

van Gunsteren, WF ;

Mark, AE .

JOURNAL OF MOLECULAR BIOLOGY, 1998, 280 (05) :925-932

[5] FREE-ENERGY DETERMINATION OF POLYPEPTIDE CONFORMATIONS GENERATED BY MOLECULAR-DYNAMICS [J].

DINOLA, A ;

BERENDSEN, HJC ;

EDHOLM, O .

MACROMOLECULES, 1984, 17 (10) :2044-2050

[6]

Gunsteren W.F.V., 1996, Biomolecular Simulation: The GROMOS96 Manual and User Guide

[7] THE LENNARD-JONES EQUATION OF STATE REVISITED [J].

JOHNSON, JK ;

ZOLLWEG, JA ;

GUBBINS, KE .

MOLECULAR PHYSICS, 1993, 78 (03) :591-618

[8] MOLECULAR-DYNAMICS SIMULATIONS IN BIOLOGY [J].

KARPLUS, M ;

PETSKO, GA .

NATURE, 1990, 347 (6294) :631-639

[9]

KARPLUS M, 1981, MACROMOLECULES, V14, P325, DOI 10.1021/ma50003a019

[10]

MARK AE, 1998, ENCY COMPUTATIONAL C, V2, P1070

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