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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 303190, 9 pages
Methodology Report

Studying Interactions by Molecular Dynamics Simulations at High Concentration

1Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, Italy
2Divisione Biomolecole, Istituto Nazionale Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Roma, Italy
3Dipartimento di Chimica Biologica, Università di Padova, Viale G. Colombo 3, 35121 Padova, Italy
4Dipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121 Padova, Italy

Received 14 July 2011; Revised 23 November 2011; Accepted 24 November 2011

Academic Editor: Paolo Ruggerone

Copyright © 2012 Federico Fogolari et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.