Integration methods for molecular dynamics

Conference · Tue Dec 31 00:00:00 EST 1996

OSTI ID:495294

Leimkuhler, B J ^[1]; Reich, S ^[2]; Skeel, R D ^[3]

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1. Univ. of Kansas, Lawrence, KS (United States)
2. Konrad-Zuse Zentrum, Berlin (Germany)
3. Univ. of Illinois, Urbana, IL (United States)

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.

• OSTI ID: 495294
• Report Number(s): CONF-9407205-Vol.82; TRN: 97:003313-0010
• Resource Relation: 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.
• Country of Publication: United States
• Language: English

Related Subjects

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