Advanced

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

Favrin, Giorgio LU ; Irbäck, Anders LU and Sjunnesson, Fredrik LU (2001) In Journal of Chemical Physics 114(8). p.8154-8158
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 3 compared to the unbiased b = 0 case. The method may be useful for kinetic studies, too.
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
114
issue
8
pages
8154 - 8158
publisher
American Institute of Physics
external identifiers
  • scopus:0035826575
ISSN
0021-9606
DOI
10.1063/1.1364637
language
English
LU publication?
yes
id
8187f2a3-3450-40c9-a916-bcb9b55bb6d8 (old id 467778)
date added to LUP
2007-08-09 11:33:17
date last changed
2018-02-18 03:36:14
@article{8187f2a3-3450-40c9-a916-bcb9b55bb6d8,
  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 3 compared to the unbiased b = 0 case. The method may be useful for kinetic studies, too.},
  author       = {Favrin, Giorgio and Irbäck, Anders and Sjunnesson, Fredrik},
  issn         = {0021-9606},
  language     = {eng},
  number       = {8},
  pages        = {8154--8158},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space},
  url          = {http://dx.doi.org/10.1063/1.1364637},
  volume       = {114},
  year         = {2001},
}