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Molecular dynamics - Definition and Overview |
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Molecular dynamics (MD) simulation numerically solves Newton's equations of motion on an atomistic or similar model of a molecular system to obtain information about its time-dependent properties.
Applications
Beginning in theoretical physics, the method of MD gained popularity in material science and since the 1970s also in biochemistry and biophysics. It serves as an important tool in protein structure determination and refinement (see also crystallography, NMR).
The interaction between the objects is either described by a force field (classical MD), a
quantum chemical model, or a mix between the two.
Popular software packages for MD simulation of biological molecules include: AMBER, CHARMM (and the commercial version CHARMm), GROMACS, GROMOS, and NAMD.
References
- J. A. McCammon, S. C. Harvey (1987) Dynamics of Proteins and Nucleic Acids. Cambridge University Press. ISBN 0-52-135652-0 (paperback); ISBN 0-52-130750 (hardback).
- M. P. Allen, D. J. Tildesley (1989) Computer simulation of liquids. Oxford University Press. ISBN 0198556454.
- D. C. Rapaport (1996) The Art of Molecular Dynamics Simulation. ISBN 0521445612.
- Daan Frenkel, Berend Smit (2001) Understanding Molecular Simulation. Academic Press. ISBN 0122673514.
- Oren M. Becker, Alexander D. Mackerell Jr, Benoît Roux, Masakatsu Watanabe (2001) Computational Biochemistry and Biophysics. Marcel Dekker. ISBN 082470455X.
- Tamar Schlick (2002) Molecular Modeling and Simulation. Springer. ISBN 038795404X.
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