The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of V on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.
Titolo: | Use of the Metropolis algorithm to simulate the dynamics of protein chains |
Autori: | TIANA, GUIDO (Primo) SUTTO, LUDOVICO (Secondo) BROGLIA, RICARDO AMERICO (Ultimo) |
Parole Chiave: | Metropolis dynamics; Protein folding |
Settore Scientifico Disciplinare: | Settore FIS/04 - Fisica Nucleare e Subnucleare Settore FIS/03 - Fisica della Materia |
Data di pubblicazione: | 2007 |
Rivista: | |
Tipologia: | Article (author) |
Digital Object Identifier (DOI): | 10.1016/j.physa.2007.02.044 |
Appare nelle tipologie: | 01 - Articolo su periodico |