Introduction to Molecular Dynamics Simulation.pdf


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John von Neumann Institute puting
Introduction to Molecular Dynamics Simulation
Michael P. Allen
published in
Computational Soft Matter: From Synthetic Polymers to Proteins,
Lecture Notes,
Norbert Attig, Kurt Binder, Helmut Grubmuller¨ , Kurt Kremer (Eds.),
John von Neumann Institute puting, Julich,¨
NIC Series, Vol. 23, ISBN 3-00-012641-4, pp. 1-28, 2004.
c 2004 by John von Neumann Institute puting

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.de/nic-series/volume23
Introduction to Molecular Dynamics Simulation
Michael P. Allen
Centre for puting and Department of Physics,
University of Warwick, Coventry CV4 7AL, United Kingdom
E-mail: .******@
In this chapter a summary is given of the key ingredients necessary to carry out a molecular
dynamics simulation, with particular emphasis on macromolecular systems. We discuss the
form of the intermolecular potential for posed of atoms, and of non-spherical
sub-units, giving examples of how pute the forces and torques. We also describe some
of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the
size of systems, and length of runs, that are needed to calculate statistical properties.
1 The Aims of Molecular Dynamics
We carry puter simulations in the hope of understanding the properties of assem-
blies of molecules in terms of their structure and the microscopic interactions between
them. This serves as plement to conventional experiments, enabling us to learn
something new, something that cannot be found out in other ways. The two main families
of simulation technique are molecular dynamics (MD) and Monte Carlo (MC); addition-

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