Generalized verlet algorithm for efficient molecular dynamics simulations with long-range interactions

Molecular Simulation

Volumn 6, Issue 1-3, 1991, Pages 121-142

  GrubmuLler H ^a   Heller, H ^a   Windemuth, A ^a   Schulten, K ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84963146276     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927029108022142     Document Type: Article

References (15)

1. H. Heller, H. Grubmöuller, and K. Schulten, “Molecular dynamics simulation on a parallel computer”, Molecular Simulation, 5 (3,4), 133-165 (1989).
2. H. Heller, “Dynamiksimulation sehr großer Makromoleköule am Beispiel des photosynthetischen Reaktionszentrums von Rhodopseudomonas viridis”, Master's thesis, Technical Universtiy of Munich, Physics Department, T 30, 1988.
3. H. Grubmöller, “Dynamiksimulation sehr großer Makromoleköule auf einem Parallelrechner”, Master's thesis, Technical University of Munich, Physics Department, T30, 1989.
4. A. R.C. Raine, D. Fincham, and W. Smith, “Systolic loop methods for molecular dynamics simulation using multiple Transputers”, Comput. Phys. Commun., 55, 13-30 (1989).
5. D. Fincham, “Parallel computers and molecular simulation”, Molecular Simulation, 1 (1,2), 1-45 (1987).
6. W. B. Streett and D. J. Tildesley, “Multiple time-step methods in molecular dynamics”, Molecular Physics, 35(3), 639-648 (1978).
7. M. P. Allen and D. J. Tildesley. “Computer Simulation of Liquids”. Clarendon Press, Oxford, 1987.
8. L. Verlet, “Computer ‘experiments’ on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules”, Physical Review, 159 (1), 98-103 (1967).
9. A. Windemuth, “Dynamiksimulation von Makromolekölen”, Master's thesis, Technical University of Munich, Physics Department, T30, James-Franck-Street, 8046 Garching, August 1988, in this work the conventional distance class algorithm is defined as follows: the Forces for particles in distance class n are updated every 2n integration steps; between updates the forces are assumed to be constant; the distance classes are the same as defined in Table 3.
10. W. D. Hillis, “The connection machine”, Scientific American, 256 (6), 86-93 (1987).
11. J. Deisenhofer and H. Michel, “The crystal structure of the photosynthetic reaction center from Rhodopseudomonas viridis”, in The photosynthetic bacterial reaction center: Structure and dynamics. Plenum Press, London, (1987).
12. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, “CHARMM: a program for macromolecular energy, minimization, and dynamics calculations”, Journal of Computational Chemistry, 4 (2), 187-217 (1983).
13. H. Treutlein, “Molekulardynamiksimulation des Reaktionszentrums von Rhodopseudomonas viridis”, PhD thesis, Technical University of Munich, Physics Department, T 30, James-Franck-Street, 8046 Garching, (1988).
14. A. T. Brönger, “X-PLOR”, The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, P. O. Box 6666, New Haven, CT 06511, May (1988).
15. L. Greengard and V. Rohklin, “A fast algorithm for particle simulation”, Journal of Computational Physics, 73, 325-348 (1987).