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

TRAJAN: a tool for analyzing trajectories from molecular simulations

G A Worth1, C Lecuyer, R C Wade

  • 1European Molecular Biology Laboratory, Heidelberg. Germany.

Journal of Molecular Graphics
|June 1, 1996
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

On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study.

The Journal of chemical physics·2025
Same author

Non-adiabatic direct quantum dynamics using force fields: Toward solvation.

The Journal of chemical physics·2024
Same author

Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach.

Nanoscale advances·2022
Same author

Mixed-quantum-classical or fully-quantized dynamics? A unified code to compare methods.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences·2022
Same author

Pulmonary Arterial Pruning and Longitudinal Change in Percent Emphysema and Lung Function: The Genetic Epidemiology of COPD Study.

Chest·2021
Same author

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

Nature communications·2017

Analyzing complex molecular dynamics simulations is now easier with a new method. This approach partitions atomic motion into

Area of Science:

  • Computational Biology
  • Biophysics
  • Materials Science

Background:

  • Molecular dynamics (MD) simulations generate complex data, posing challenges for analysis.
  • Extracting meaningful insights into atomic motion from simulation trajectories is crucial.
  • Existing methods may not fully capture the anharmonic nature of atomic movements.

Purpose of the Study:

  • To introduce a novel method for analyzing MD simulation trajectories.
  • To extract key features of atomic motion, including anharmonicity and correlations.
  • To provide a visualization tool for simulation data analysis.

Main Methods:

  • Developed a trajectory analysis procedure (TRAJAN) for simulation data.
  • Partitioned atomic trajectories into 'conformation wells' representing harmonic oscillations.

Related Experiment Videos

  • Quantified inter-well movement, intra-well motion ellipsoids, and atomic motion correlations.

    • Main Results:

    • The TRAJAN method successfully analyzes complex simulation data.
    • It quantifies atomic motion characteristics, including anharmonic transitions between wells.
    • Results can be visualized using molecular graphics for intuitive understanding.

    Conclusions:

    • The TRAJAN procedure offers a robust method for analyzing simulation trajectories.
    • It is applicable to various simulation types, including equilibrium and nonequilibrium MD.
    • This approach enhances the extraction of dynamic information from complex biological and material systems.