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Multioverlap simulations for transitions between reference configurations.

Bernd A Berg1, Hiroshi Noguchi, Yuko Okamoto

  • 1Department of Physics, Florida State University, Tallahassee, Florida 32306, USA. berg@csit.fsu.edu

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|October 4, 2003
PubMed
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This study introduces a novel procedure to overcome free-energy barriers by adjusting probability densities. Simulations of Met-enkephalin demonstrate the method

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biophysics

Background:

  • Free-energy barriers in molecular systems hinder conformational transitions.
  • Simulating rare events requires efficient methods to overcome these barriers.

Purpose of the Study:

  • To develop a procedure for constructing weight factors to flatten probability densities.
  • To enable overcoming free-energy barriers in overlap variables.
  • To generalize the approach for inducing transitions between two reference configurations.

Main Methods:

  • Introduction of a procedure to construct weight factors.
  • Generalization to handle overlaps with respect to two reference configurations.
  • Simulations of Met-enkephalin using the ECEPP/2 energy function.

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Main Results:

  • The method successfully flattens probability densities, overcoming free-energy barriers.
  • Transitions between global-energy-minimum and second lowest-energy states of Met-enkephalin were induced.
  • Free energy was computed as a function of dihedral and root-mean-square distances.

Conclusions:

  • The developed procedure effectively overcomes free-energy barriers in molecular simulations.
  • The approach allows for the identification of transition states and estimation of free-energy barriers.
  • This method is valuable for studying conformational transitions in peptides like Met-enkephalin.