Long time dynamics of complex systems

被引：73

作者：

Elber, R ^{[1
]}

Ghosh, A ^{[1
]}

Cárdenas, A ^{[1
]}

机构：

[1] Cornell Univ, Dept Comp Sci, Ithaca, NY 14853 USA

来源：

ACCOUNTS OF CHEMICAL RESEARCH | 2002年 / 35卷 / 06期

关键词：

D O I：

10.1021/ar010021d

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Molecular dynamics trajectories of large biological molecules are restricted to nanoseconds. We describe a computational method, based on optimization of a functional, to extend the time of molecular simulations by orders of magnitude. Variants of our technique have already produced microsecond and millisecond trajectories. The large steps enable feasible computations of atomically detailed approximate trajectories. Numerical examples are provided: (i) a conformational change in blocked glycine peptide and (ii) helix formation of an alanine-rich peptide.

引用

页码：396 / 403

页数：8

共 25 条

[1] Collective protein dynamics in relation to function
Berendsen, HJC
Hayward, S
[J]. CURRENT OPINION IN STRUCTURAL BIOLOGY, 2000, 10 (02) : 165 - 169
[2] CZERMINSKI R, 1990, INT J QUANTUM CHEM, P167
[3] Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
Duan, Y
Kollman, PA
[J]. SCIENCE, 1998, 282 (5389) : 740 - 744
[4] MOIL - A PROGRAM FOR SIMULATIONS OF MACROMOLECULES
ELBER, R
ROITBERG, A
SIMMERLING, C
GOLDSTEIN, R
LI, HY
VERKHIVKER, G
KEASAR, C
ZHANG, J
ULITSKY, A
[J]. COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) : 159 - 189
[5] Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide
Elber, R
Meller, J
Olender, R
[J]. JOURNAL OF PHYSICAL CHEMISTRY B, 1999, 103 (06): : 899 - 911
[6] A METHOD FOR DETERMINING REACTION PATHS IN LARGE MOLECULES - APPLICATION TO MYOGLOBIN
ELBER, R
KARPLUS, M
[J]. CHEMICAL PHYSICS LETTERS, 1987, 139 (05) : 375 - 380
[7] Folding simulations of a three-stranded antiparallel β-sheet peptide
Ferrara, P
Caflisch, A
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (20) : 10780 - 10785
[8] Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators
Figueirido, F
Levy, RM
Zhou, RH
Berne, BJ
[J]. JOURNAL OF CHEMICAL PHYSICS, 1997, 106 (23) : 9835 - 9849
[9] Autoionization in liquid water
Geissler, PL
Dellago, C
Chandler, D
Hutter, J
Parrinello, M
[J]. SCIENCE, 2001, 291 (5511) : 2121 - 2124
[10] Generalized born model based on a surface integral formulation
Ghosh, A
Rapp, CS
Friesner, RA
[J]. JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (52): : 10983 - 10990

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