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What is Multi-Scale Molecular Dynamics Simulations about?

In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various components, according to the equations of Newtonian physics. Molecular Dynamics is currently mainly used in materials science and molecular biology. In this document, we limit ourselves to {\it alkanes} which are non-cyclic carbon-hydrogenated chains. In the basic ``All-atom'' (AA) scale, all the atoms are directly simulated. In the ``United-atom'' (UA) scale, one considers grains that are composed of a carbon atom with the hydrogen atoms attached to it. Grains in the ``Coarse-grained'' (CG) scale are composed of two consecutive UA grains. In the multi-scale approach, one tries to use as much as possible the UA and CG scales which can be more efficiently simulated than the AA scale. In this document, we mainly put the focus on three topics. First, we describe an MD system, implemented in the Java programming language, according to the Synchronous Reactive Programming approach in which there exists a notion of a global logical time. This system is used to

Author

Boussinot, Frédéric

Published

2024

Language

EN