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

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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.

Detaljer

Författare
Enheter & grupper
Forskningsområden

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Biofysik
Originalspråkengelska
Sidor (från-till)8154-8158
TidskriftJournal of Chemical Physics
Volym114
Utgivningsnummer8
StatusPublished - 2001
PublikationskategoriForskning
Peer review utfördJa

Relaterad forskningsoutput

Favrin, G., 2004, Lund University. 124 s.

Forskningsoutput: AvhandlingDoktorsavhandling (sammanläggning)

Sjunnesson, F., 2003, Department of Theoretical Physics, Lund University. 114 s.

Forskningsoutput: AvhandlingDoktorsavhandling (sammanläggning)

Visa alla (2)