Integration methods for molecular dynamics
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. 48 refs., 2 figs.
- Univ. of Kansas, Lawrence, KS (United States)
- Konrad-Zuse Zentrum, Berlin (Germany)
- Univ. of Illinois, Urbana, IL (United States)
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- Conference: IMA summer program on molecular biology, Minneapolis, MN (United States), 5-29 Jul 1994; Other Information: PBD: 1996; Related Information: Is Part Of Mathematical approaches to biomolecular structure and dynamics; Mesirov, J.P. [ed.] [Boston Univ., MA (United States). Computer Science Dept.]; Sumners, D.W. [ed.] [Florida State Univ., Tallahassee, FL (United States). Dept. of Mathematics]; Schulten, K. [ed.] [Univ. of Illinois, Urbana, IL (United States)]; PB: 262 p.
- Springer-Verlag New York, Inc., New York, NY (United States)
- Country of Publication:
- United States
- 55 BIOLOGY AND MEDICINE, BASIC STUDIES; 99 MATHEMATICS, COMPUTERS, INFORMATION SCIENCE, MANAGEMENT, LAW, MISCELLANEOUS; MOLECULES; MECHANICS; DYNAMICS; COMPUTERIZED SIMULATION; STRUCTURE-ACTIVITY RELATIONSHIPS; MOLECULAR STRUCTURE; MOLECULAR DYNAMICS METHOD; TIME DEPENDENCE; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; NUMERICAL ANALYSIS; SP GROUPS