Normal-mode analysis without the Hessian: A driven molecular-dynamics approach

被引:36
|
作者
Bowman, JM [1 ]
Zhang, XB
Brown, A
机构
[1] Emory Univ, Cherry L Emerson Ctr Sci Computat, Atlanta, GA 30322 USA
[2] Emory Univ, Dept Chem, Atlanta, GA 30322 USA
关键词
D O I
10.1063/1.1578475
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
We point out that normal modes and frequencies of molecules and molecular complexes can be obtained directly from a harmonically driven molecular dynamics calculation. We illustrate this approach for HOD and H5O2+ and then discuss its potential advantages over the standard Hessian-based approach for large molecules. (C) 2003 American Institute of Physics.
引用
收藏
页码:646 / 650
页数:5
相关论文
共 50 条
  • [41] Inhibition mechanism of the acetylcholine receptor by α-neurotoxins as revealed by normal-mode dynamics
    Samson, Abraham O.
    Levitt, Michael
    BIOCHEMISTRY, 2008, 47 (13) : 4065 - 4070
  • [42] ON THE DERIVATION OF THE QUANTUM MOLECULAR-DYNAMICS APPROACH
    AICHELIN, J
    NUCLEAR EQUATION OF STATE, PART A: DISCOVERY OF NUCLEAR SHOCK WAVES AND THE EOS, 1989, 216 : 363 - 373
  • [43] INTERFACE AMORPHIZATION - A MOLECULAR-DYNAMICS APPROACH
    GONCALVES, S
    RAMIREZ, R
    KIWI, M
    JOURNAL OF PHYSICS-CONDENSED MATTER, 1994, 6 (23) : 4213 - 4224
  • [44] Dynamic features of homodimer interfaces calculated by normal-mode analysis
    Tsuchiya, Yuko
    Kinoshita, Kengo
    Endo, Shigeru
    Wako, Hiroshi
    PROTEIN SCIENCE, 2012, 21 (10) : 1503 - 1513
  • [45] Normal-mode analysis of a baroclinic wave-mean oscillation
    Wolfe, Christopher L.
    Samelson, Roger M.
    JOURNAL OF THE ATMOSPHERIC SCIENCES, 2006, 63 (11) : 2795 - 2812
  • [46] An approach to detect afterslips in giant earthquakes in the normal-mode frequency band
    Tanimoto, Toshiro
    Ji, Chen
    Igarashi, Mitsutsugu
    GEOPHYSICAL JOURNAL INTERNATIONAL, 2012, 190 (02) : 1097 - 1110
  • [47] THE EFFECTS OF SOLVENT ON THE CONFORMATION AND THE COLLECTIVE MOTIONS OF PROTEIN - NORMAL MODE ANALYSIS AND MOLECULAR-DYNAMICS SIMULATIONS OF MELITTIN IN WATER AND IN VACUUM
    KITAO, A
    HIRATA, F
    GO, N
    CHEMICAL PHYSICS, 1991, 158 (2-3) : 447 - 472
  • [48] Inherent flexibility of calmodulin domains: A normal-mode analysis study
    Barton, NP
    Verma, CS
    Caves, LSA
    JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (42) : 11036 - 11040
  • [49] AN ANALYSIS OF NEARFIELD NORMAL-MODE AMPLITUDE ANOMALIES OF THE LANDERS EARTHQUAKE
    WATADA, S
    KANAMORI, H
    ANDERSON, DL
    GEOPHYSICAL RESEARCH LETTERS, 1993, 20 (23) : 2611 - 2614
  • [50] NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method
    Hoffmann, Alexandre
    Gradinin, Sergei
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (05) : 2123 - 2134