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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space

Author

  • Giorgio Favrin
  • Anders Irbäck
  • Fredrik Sjunnesson

Summary, in English

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and the Ramachandran torsion angles as its only degrees of freedom, for different b. Without excessive fine tuning, we find that the effective step size can be increased by a factor of 3 compared to the unbiased b = 0 case. The method may be useful for kinetic studies, too.

Department/s

  • Computational Biology and Biological Physics

Publishing year

2001

Language

English

Pages

8154-8158

Publication/Series

Journal of Chemical Physics

Volume

114

Issue

8

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Topic

  • Biophysics

Status

Published

ISBN/ISSN/Other

  • ISSN: 0021-9606