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Obtaining fully dynamic coarse-grained models from MD.

Pep Español1, Ignacio Zúñiga

  • 1Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141 E-28080, Madrid, Spain. pep@fisfun.uned.esc

Physical Chemistry Chemical Physics : PCCP
|March 29, 2011
PubMed
Summary
This summary is machine-generated.

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We developed a general method to create accurate models for molecular systems using Fokker-Planck equations. This approach minimizes relative entropy, ensuring the model captures the full dynamics of coarse-grained descriptions.

Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Molecular dynamics

Background:

  • Coarse-grained models simplify complex molecular systems.
  • Fokker-Planck equations describe system dynamics.
  • Parameterizing these equations accurately is challenging.

Purpose of the Study:

  • To present a general method for parameterizing drift and diffusion terms in Fokker-Planck equations for coarse-grained molecular systems.
  • To capture the full dynamics of the coarse-grained description.
  • To provide a robust methodology for model development.

Main Methods:

  • Minimization of relative entropy using two-time joint probability.
  • Bayesian inference starting from diffusion process path probability.

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  • Derivation of an optimization function common to both approaches.

    • Main Results:

    • A general method for obtaining parametrised drift and diffusion terms for Fokker-Planck equations.
    • Demonstration that both relative entropy minimization and Bayesian inference yield the same optimization function.
    • Heuristic argument connecting the two presented approaches.

    Conclusions:

    • The presented methodology offers a robust way to derive parametrised models for coarse-grained molecular systems.
    • The convergence of two distinct theoretical frameworks (relative entropy and Bayesian inference) validates the approach.
    • This work provides a strong foundation for accurate modeling of molecular dynamics at coarse-grained levels.