A dielectric continuum molecular dynamics method

M. Marchi, D. Borgis, N. Levy, Pietro Ballone

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of the functional, we construct the equations of motion for the system based on a Car-Parrinello technique. In the limit of the adiabatic evolution of the polarization field variables, our method provides the solution of the dielectric continuum problem "on the fly," while the molecular coordinates are propagated. In this first study, we show how our dielectric continuum molecular dynamics method can be successfully applied to hydrated biomolecules, with low cost compared to free energy simulations with explicit solvent. To our knowledge, this is the first time that stable and conservative molecular dynamic simulations of solutes can be performed for a dielectric continuum model of the solvent. (C) 2001 American Institute of Physics.
Original languageEnglish
Pages (from-to)4377-4385
Number of pages9
JournalJournal of Chemical Physics
Volume114
Issue number10
DOIs
Publication statusPublished - 08 Mar 2001

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Molecular dynamics
molecular dynamics
continuums
Polarization
Free energy
polarization
free energy
Biomolecules
Macromolecules
macromolecules
Equations of motion
Electrostatics
solutes
equations of motion
Railroad cars
simulation
degrees of freedom
electrostatics
expansion
Computer simulation

Cite this

Marchi, M., Borgis, D., Levy, N., & Ballone, P. (2001). A dielectric continuum molecular dynamics method. Journal of Chemical Physics, 114(10), 4377-4385. https://doi.org/10.1063/1.1348028
Marchi, M. ; Borgis, D. ; Levy, N. ; Ballone, Pietro. / A dielectric continuum molecular dynamics method. In: Journal of Chemical Physics. 2001 ; Vol. 114, No. 10. pp. 4377-4385.
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Marchi, M, Borgis, D, Levy, N & Ballone, P 2001, 'A dielectric continuum molecular dynamics method', Journal of Chemical Physics, vol. 114, no. 10, pp. 4377-4385. https://doi.org/10.1063/1.1348028

A dielectric continuum molecular dynamics method. / Marchi, M.; Borgis, D.; Levy, N.; Ballone, Pietro.

In: Journal of Chemical Physics, Vol. 114, No. 10, 08.03.2001, p. 4377-4385.

Research output: Contribution to journalArticle

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Marchi M, Borgis D, Levy N, Ballone P. A dielectric continuum molecular dynamics method. Journal of Chemical Physics. 2001 Mar 8;114(10):4377-4385. https://doi.org/10.1063/1.1348028