IMR Press / FBL / Volume 19 / Issue 4 / DOI: 10.2741/4229

Frontiers in Bioscience-Landmark (FBL) is published by IMR Press from Volume 26 Issue 5 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Review
Molecular mechanics and dynamics: numerical tools to sample the configuration space
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1 Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
2 Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
Academic Editor:Andrea Cavalli
Front. Biosci. (Landmark Ed) 2014, 19(4), 578–604; https://doi.org/10.2741/4229
Published: 1 January 2014
(This article belongs to the Special Issue Computational medicinal chemistry and drug design)
Abstract

Molecular simulation is increasingly used in many theoretical as well applicative fields in both Life and Material sciences. It relies on the capability of estimating the forces acting both inter- and intra-molecularly, providing configurations of minimum energy and sampling the configurational space consistently with the main statistical ensembles. In this context, the engine that approximates the temporal evolution and the force field that expresses the instantaneously occurring forces, i.e. Molecular Dynamics and Molecular Mechanics, respectively, are the crucial bases that need to be known and handled. Here, the fundamentals of these tools are provided, with particular attention to numerical and simulative aspects.

Keywords
Molecular mechanics
Molecular Dynamics
Force Fields
Polarizable Force Fields
Configurational Space
Atomistic Simulation
Review
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