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Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, viale Regina Margherita 261, 00198 Rome, Italy
Briefings in Bioinformatics, 2017

@article{biagini2017molecular,

   title={Molecular dynamics recipes for genome research},

   author={Biagini, Tommaso and Chillemi, Giovanni and Mazzoccoli, Gianluigi and Grottesi, Alessandro and Fusilli, Caterina and Capocefalo, Daniele and Castellana, Stefano and Vescovi, Angelo Luigi and Mazza, Tommaso},

   journal={Briefings in Bioinformatics},

   pages={bbx006},

   year={2017},

   publisher={Oxford University Press}

}

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Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on high performance computing (HPC) devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect.
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