Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A sampling problem in molecular dynamics simulations of macromolecules

J B Clarage1, T Romo, B K Andrews

  • 1Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 11, 1995
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The contribution of electrostatic interactions to the collapse of oligoglycine in water.

Condensed matter physics·2017
Same author

[Endoscopic brow lift].

HNO·2012
Same author

The theoretical basis of universal identification systems for bacteria and viruses.

Journal of biological physics and chemistry : JBPC·2010
Same author

Motions of tropomyosin: characterization of anisotropic motions and coupled displacements in crystals.

Biophysical journal·2009
Same author

Fast multipole methods for particle dynamics.

Molecular simulation·2009
Same author

Biomedical informatics training at the University of Wisconsin-Madison.

Yearbook of medical informatics·2007
Same journal

Costunolide ameliorates autoimmune uveitis by targeting USP15 to suppress TNF-α-induced retinal endothelial inflammation.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

A ligandable PNT domain establishes ERG as a directly targetable oncogenic driver in prostate cancer.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Identification of cellular intermediates unveils unique enzymes for flagellar glycan biosynthesis in <i>Clostridioides difficile</i>.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

The structure of correlated variability reflects task-relevant information in sensory neurons.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Shared neurogenetic substrates of nonplanning impulsivity and procrastination.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

HIV-1 capsid interactions with Nuclear Pore Complex components support nuclear entry via affinity gradient.

Proceedings of the National Academy of Sciences of the United States of America·2026
See all related articles

Molecular dynamics simulations undersample atomic displacement correlations at the 1 ns timescale. This limitation affects the accuracy of macromolecular fluctuation analysis across different representations, including crystallography and configuration space.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Molecular dynamics (MD) simulations are crucial for studying macromolecular motions.
  • Accurately capturing low-frequency atomic displacements is essential for understanding protein dynamics.
  • Current simulation timescales may not fully capture the relevant conformational landscape.

Purpose of the Study:

  • To assess the adequacy of 1 ns molecular dynamics simulations for capturing low-frequency atomic displacement correlations.
  • To evaluate the impact of undersampling on different representations of macromolecular fluctuations.
  • To visualize the extent of phase space sampling in protein dynamics.

Main Methods:

  • Analysis of atomic displacement correlations from 1 ns MD simulations.

Related Experiment Videos

  • Comparison across three representations: diffuse X-ray scattering (reciprocal space), covariance matrices (Cartesian space), and dimensionally reduced projections (configuration space).
  • Utilizing diffuse X-ray scattering data and covariance matrices to analyze macromolecular fluctuations.

    • Main Results:

    • Low-frequency atomic displacement correlations are undersampled within 1 ns MD simulations.
    • The extent of phase space sampling varies significantly across different representations.
    • Crystallographic and Cartesian space analyses may not fully reflect the sampled conformational space.

    Conclusions:

    • 1 ns MD simulations are insufficient for comprehensively characterizing low-frequency atomic displacement correlations in macromolecules.
    • Careful consideration of phase space sampling is required when interpreting MD simulation results.
    • Further development in simulation techniques or analysis methods is needed to overcome timescale limitations.