English

Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space

Soft Condensed Matter 2009-11-07 v1 Chemical Physics

Abstract

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 three compared to the unbiased b=0 case. The method may be useful for kinetic studies, too.

Keywords

Cite

@article{arxiv.cond-mat/0103580,
  title  = {Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space},
  author = {Giorgio Favrin and Anders Irbäck and Fredrik Sjunnesson},
  journal= {arXiv preprint arXiv:cond-mat/0103580},
  year   = {2009}
}

Comments

14 pages, 4 figures