title: Studying interactions by molecular dynamics simulations at high concentration.
abstract: Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.
authors.affiliation: Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Udine, Italy. federico.fogolari@uniud.it
authors.forename: Federico
authors.initials: F
authors.lastname: Fogolari
authors.forename: Alessandra
authors.initials: A
authors.lastname: Corazza
authors.forename: Stefano
authors.initials: S
authors.lastname: Toppo
authors.forename: Silvio C E
authors.initials: SC
authors.lastname: Tosatto
authors.forename: Paolo
authors.initials: P
authors.lastname: Viglino
authors.forename: Fulvio
authors.initials: F
authors.lastname: Ursini
authors.forename: Gennaro
authors.initials: G
authors.lastname: Esposito
mesh_terms: D000465:Algorithms; D004058:Diffusion; D005979:Glutathione Peroxidase / Q000737:chemistry; D006861:Hydrogen Peroxide / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D001613:beta 2-Microglobulin / Q000737:chemistry
chemical_list: D001613:beta 2-Microglobulin; D006861:Hydrogen Peroxide; D005979:Glutathione Peroxidase