A sampling problem in molecular dynamics simulations of macromolecules

J. B. Clarage, T. Romo, B. K. Andrews, Bernard Pettitt, G. N. Phillips

Research output: Contribution to journalArticle

151 Citations (Scopus)

Abstract

Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.

Original languageEnglish (US)
Pages (from-to)3288-3292
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume92
Issue number8
StatePublished - 1995
Externally publishedYes

Fingerprint

Crystallography
Molecular Dynamics Simulation
X-Rays
Proteins

Keywords

  • crystallography
  • dynamical systems
  • phase space
  • protein flexibility
  • x-ray diffuse scattering

ASJC Scopus subject areas

  • General
  • Genetics

Cite this

A sampling problem in molecular dynamics simulations of macromolecules. / Clarage, J. B.; Romo, T.; Andrews, B. K.; Pettitt, Bernard; Phillips, G. N.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 92, No. 8, 1995, p. 3288-3292.

Research output: Contribution to journalArticle

@article{ad0a661fcd3a48259a8901e0565c5987,
title = "A sampling problem in molecular dynamics simulations of macromolecules",
abstract = "Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.",
keywords = "crystallography, dynamical systems, phase space, protein flexibility, x-ray diffuse scattering",
author = "Clarage, {J. B.} and T. Romo and Andrews, {B. K.} and Bernard Pettitt and Phillips, {G. N.}",
year = "1995",
language = "English (US)",
volume = "92",
pages = "3288--3292",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "8",

}

TY - JOUR

T1 - A sampling problem in molecular dynamics simulations of macromolecules

AU - Clarage, J. B.

AU - Romo, T.

AU - Andrews, B. K.

AU - Pettitt, Bernard

AU - Phillips, G. N.

PY - 1995

Y1 - 1995

N2 - Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.

AB - Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.

KW - crystallography

KW - dynamical systems

KW - phase space

KW - protein flexibility

KW - x-ray diffuse scattering

UR - http://www.scopus.com/inward/record.url?scp=0028912595&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0028912595&partnerID=8YFLogxK

M3 - Article

VL - 92

SP - 3288

EP - 3292

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 8

ER -