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

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.

• Författare: Giorgio Favrin; Anders Irbäck; Fredrik Sjunnesson
• Avdelning/ar: Beräkningsbiologi och biologisk fysik - Har omorganiserats
• Publiceringsår: 2001
• Språk: Engelska
• Sidor: 8154-8158
• Publikation/Tidskrift/Serie: Journal of Chemical Physics
• Volym: 114
• Issue: 8
• Länkar: http://dx.doi.org/10.1063/1.1364637
• Dokumenttyp: Artikel i tidskrift
• Förlag: American Institute of Physics (AIP)
• Ämne: Biophysics
• Status: Published
• ISBN/ISSN/Övrigt: ISSN: 0021-9606