The description of the dynamics of a complex, high-dimensional system in terms of a low-dimensional set of collective variables Y can be fruitful if the low-dimensional representation satisfies a Langevin equation with drift and diffusion coefficients that depend only on Y . We present a computational scheme to evaluate whether a given collective variable provides a faithful low-dimensional representation of the dynamics of a high-dimensional system. The scheme is based on the framework of a finite-difference Langevin equation, similar to that used for molecular-dynamics simulations. This allows one to calculate the drift and diffusion coefficients in any point of the full-dimensional system. The width of the distribution of drift and diffusion coefficients in an ensemble of microscopic points at the same value of Y indicates to what extent the dynamics of Y is described by a simple Langevin equation. Using a simple protein model, we show that collective variables often used to describe biopolymers display a non-negligible width both in the drift and in the diffusion coefficients. We also show that the associated effective force is compatible with the equilibrium free energy calculated from a microscopic sampling, but it results in markedly different dynamical properties.

Properties of low-dimensional collective variables in the molecular dynamics of biopolymers / R. Meloni, C. Camilloni, G. Tiana. - In: PHYSICAL REVIEW. E. - ISSN 2470-0045. - 94:5(2016), pp. 052406.1-052406.13. [10.1103/PhysRevE.94.052406]

Properties of low-dimensional collective variables in the molecular dynamics of biopolymers

R. Meloni
Primo
;
C. Camilloni;G. Tiana
2016

Abstract

The description of the dynamics of a complex, high-dimensional system in terms of a low-dimensional set of collective variables Y can be fruitful if the low-dimensional representation satisfies a Langevin equation with drift and diffusion coefficients that depend only on Y . We present a computational scheme to evaluate whether a given collective variable provides a faithful low-dimensional representation of the dynamics of a high-dimensional system. The scheme is based on the framework of a finite-difference Langevin equation, similar to that used for molecular-dynamics simulations. This allows one to calculate the drift and diffusion coefficients in any point of the full-dimensional system. The width of the distribution of drift and diffusion coefficients in an ensemble of microscopic points at the same value of Y indicates to what extent the dynamics of Y is described by a simple Langevin equation. Using a simple protein model, we show that collective variables often used to describe biopolymers display a non-negligible width both in the drift and in the diffusion coefficients. We also show that the associated effective force is compatible with the equilibrium free energy calculated from a microscopic sampling, but it results in markedly different dynamical properties.
diffusion-coefficients; dependent diffusion; bayesian-analysis; protein; simulations; coordinate
Settore FIS/03 - Fisica della Materia
2016
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/453878
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