The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Δt used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than Δt, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps Δt. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein.

Faccioli, P. (2010). Molecular Dynamics at Low Time Resolution. THE JOURNAL OF CHEMICAL PHYSICS, 133(16) [10.1063/1.3493459].

Molecular Dynamics at Low Time Resolution

Faccioli, Pietro
2010

Abstract

The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Δt used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than Δt, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps Δt. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein.
Articolo in rivista - Articolo scientifico
Renormalization group and molecular dynamics
English
2010
133
16
164106
none
Faccioli, P. (2010). Molecular Dynamics at Low Time Resolution. THE JOURNAL OF CHEMICAL PHYSICS, 133(16) [10.1063/1.3493459].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/405649
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