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Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
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Equipartition Principle for Internal Coordinate Molecular Dynamics.

Abhinandan Jain1, In-Hee Park, Nagarajan Vaidehi

  • 1Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109, USA , and Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.

Journal of Chemical Theory and Computation
|January 24, 2013
PubMed
Summary

A new equipartition principle for internal coordinate molecular dynamics (ICMD) simulations is introduced using non-canonical modal coordinates. This principle enables rigorous velocity initialization and entropy calculations in ICMD, overcoming limitations of Cartesian models.

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Area of Science:

  • Computational chemistry and physics
  • Molecular dynamics simulations
  • Statistical mechanics

Background:

  • The equipartition principle in Cartesian molecular dynamics assigns kinetic energy per degree of freedom.
  • Internal coordinate molecular dynamics (ICMD) lacks a direct equipartition principle due to coupled generalized coordinates and cross-terms.
  • Current ICMD velocity initialization methods are often ad hoc.

Purpose of the Study:

  • To develop a new equipartition principle applicable to internal coordinate molecular dynamics (ICMD) models.
  • To introduce non-canonical modal coordinates to simplify ICMD structure and recover equipartition properties.
  • To establish a rigorous foundation for velocity initialization and entropy calculations in ICMD.

Main Methods:

  • Introduction of non-canonical modal coordinates for ICMD.
  • Derivation of recursive algorithms for transforming between modal and physical coordinates.
  • Development of a new equipartition principle based on modal coordinates.

Main Results:

  • A novel equipartition principle for ICMD simulations in modal coordinates has been established.
  • Efficient computational algorithms for coordinate transformations were derived.
  • The new principle provides a rigorous method for initializing velocities in ICMD.

Conclusions:

  • The developed equipartition principle offers a rigorous approach for ICMD velocity initialization, replacing previous ad hoc methods.
  • This work lays the groundwork for accurate conformational entropy calculations using ICMD.
  • The use of modal coordinates simplifies ICMD while retaining essential physical properties.