A fast recursive algorithm for molecular dynamics simulation

• Published in: Journal of computational physics Vol. 106; no. 2; pp. 258 - 268
• Main Authors: Jain, A., Vaidehi, N., Rodriguez, G.
• Format: Journal Article
• Language: English
• Published: Legacy CDMS Elsevier 01.06.1993
• Subjects: 990200 > Mathematics & Computers; ALGORITHMS; CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; COMPUTERIZED SIMULATION; DEGREES OF FREEDOM; DIFFERENTIAL EQUATIONS; DYNAMICS; EQUATIONS; EQUATIONS OF MOTION; Exact sciences and technology; FACTORIZATION; GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; Inorganic And Physical Chemistry; MATHEMATICAL LOGIC; Mathematical methods in physics; MATRICES; MECHANICS; Numerical approximation and analysis; NUMERICAL SOLUTION; PARTIAL DIFFERENTIAL EQUATIONS; Physics; SIMULATION 661300 > Other Aspects of Physical Science > (1992-); Freedom degree; Equation of motion; Molecular structure; Molecular dynamics; Fast algorithm; Dynamic model; Recursive algorithm; Solution
• ISSN: 0021-9991; 1090-2716
• DOI: 10.1006/jcph.1993.1106

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.