Two algorithms to compute projected correlation functions in molecular dynamics simulations.
An explicit derivation of the Mori-Zwanzig orthogonal dynamics of observables is presented and leads to two practical algorithms to compute exactly projected observables (e.g., random noise) and projected correlation function (e.g., memory kernel) from a molecular dynamics trajectory. The algorithms are then applied to study the diffusive dynamics of a tagged particle in a Lennard-Jones fluid, the properties of the associated random noise, and a decomposition of the corresponding memory kernel.
Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX, F-75005 Paris, France.
Antoine
A
Carof
UMR 8640 CNRS-ENS-UPMC PASTEUR, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris, France and UPMC Univ Paris 06, UMR 8640 CNRS-ENS-UPMC PASTEUR, F-75005 Paris, France.
Rodolphe
R
Vuilleumier
Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX, F-75005 Paris, France.
Benjamin
B
Rotenberg
D000465:Algorithms; D056004:Molecular Dynamics Simulation