Abstract
Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches.
Key words
The work of the first author was performed under grant number NSF Grant DMS-9303223 and relied on resources of the Kansas Institute for Theoretical and Computational Science. The work of the second and third authors was performed at the Beck-man Institute of the University of Illinois and supported in part by DOE/NSF grant DE-FG02–91-ER25099/DMS-9304268, by NIH Grant P41RR05969, and by NSF/ARPA Grant ASC-9318159
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Leimkuhler, B.J., Reich, S., Skeel, R.D. (1996). Integration Methods for Molecular Dynamics. In: Mesirov, J.P., Schulten, K., Sumners, D.W. (eds) Mathematical Approaches to Biomolecular Structure and Dynamics. The IMA Volumes in Mathematics and its Applications, vol 82. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-4066-2_10
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DOI: https://doi.org/10.1007/978-1-4612-4066-2_10
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