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

Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters.

Pablo Nigra1, David L Freeman, J D Doll

  • 1Department of Chemistry, University of Rhode Island, Kingston, 02881, USA.

The Journal of Chemical Physics
|April 20, 2005
PubMed
Summary

This study enhances the smart-darting Monte Carlo method for simulations, improving calculations of heat capacity for Lennard-Jones clusters by reducing statistical fluctuations during isomerization.

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

Thermodynamic integration methods, infinite swapping, and the calculation of generalized averages.

The Journal of chemical physics·2017
Same author

Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping.

Journal of chemical theory and computation·2015
Same author

Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules.

Journal of chemical theory and computation·2015
Same author

On performance measures for infinite swapping Monte Carlo methods.

The Journal of chemical physics·2015
Same author

Growth analysis of corn and soybean response to allelopathic effects of weed residues at various temperatures and photosynthetic photon flux densities.

Journal of chemical ecology·2014
Same author

Rare-event sampling: occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods.

The Journal of chemical physics·2012

Area of Science:

  • Computational Chemistry
  • Statistical Mechanics
  • Molecular Dynamics

Background:

  • Quasiergodicity problems in simulations arise from high energy barriers between configuration spaces.
  • Original smart-darting algorithm struggles with unrestricted rotational motion and permutational isomerism, leading to low acceptance probabilities.
  • Efficient simulation of complex molecular systems requires methods that overcome these limitations.

Purpose of the Study:

  • To combine the smart-darting algorithm with parallel tempering for improved molecular simulations.
  • To modify the smart-darting algorithm to handle unrestricted rotation and permutational isomerism effectively.
  • To calculate the heat capacity of a seven-atom Lennard-Jones cluster with enhanced accuracy.

Main Methods:

Related Experiment Videos

  • Modified smart-darting algorithm using a restricted Eckart space coupled with local moves.
  • Integration of the modified smart-darting method with parallel tempering.
  • Application to the calculation of heat capacity for a seven-atom Lennard-Jones cluster.

    • Main Results:

    • The modified smart-darting method significantly reduces statistical fluctuations in heat capacity calculations, especially during isomerization.
    • Combining modified smart-darting with parallel tempering yields smaller statistical fluctuations than parallel tempering alone.
    • The enhanced method improves the accuracy of thermodynamic property calculations for molecular clusters.

    Conclusions:

    • The modified smart-darting algorithm effectively addresses limitations of the original method concerning rotational motion and isomerism.
    • The combination of smart-darting and parallel tempering offers a powerful approach for accurate simulations of complex molecular systems.
    • This improved simulation technique provides more reliable thermodynamic data for Lennard-Jones clusters.