The object-oriented development of a parallel application in protein dynamics: Why we need software tools for HPCN applications

Computer Physics Communications

Volumn 97, Issue 1-2, 1996, Pages 124-135

  Bækdal, Lars ^a   Joosen, Wouter ^a   Larsen, Thomas ^a   Kolafa, Jiri ^a   Ovesen, Jens H ^a   Perram, John W ^a   Petersen, Henrik G ^a   Bywater, Robert ^b   Ratner, Mark ^c  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b NOVO NORDISK A S   (Denmark)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; PARALLEL PROCESSING SYSTEMS; POLYELECTROLYTES; PROTEINS;

META-PROGRAM; OBJECT-ORIENTED APPLICATIONS;

COMPUTER SIMULATION;

EID: 0030564732     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/0010-4655(96)00026-4     Document Type: Article

References (12)

1. M. Saito, Molecular dynamics simulations of proteins in solution: Artefacts caused by the cutoff approximation, J. Chem. Phys. 101 (1994) 4055.
2. D.M. Beazley and P.S. Lomdahl, Large-scale molecular dynamics on massively parallel processors: Part II, SIAM News 28 (1995) 10.
3. T. Larsen, W. Joosen and J.W. Perram, The object-oriented development of a parallel application in polymer dynamics, Proc. 2nd Int. Conf. on O-O Numerics, Vol. 2 (Rogue Wave Software 1994) p. 250.
4. L. Greengard, The rapid evaluation of potential fields in particle systems (MIT Press, Cambridge, MA, 1988).
5. J.W. Perram, S.W. de Leeuw and E.R. Smith, Simulation of electrostatic systems in periodic boundary conditions: I Lattice sums and dielectric constants, Proc. Roy. Soc. A 373 (1980) 27, reviewed in M.P. Allen and D. Tildesley, Computer Simulation of Liquids (Oxford Univ. Press, Oxford, 1987).
6. J.W. Perram, S.W. de Leeuw and E.R. Smith, Simulation of electrostatic systems in periodic boundary conditions: I Lattice sums and dielectric constants, Proc. Roy. Soc. A 373 (1980) 27, reviewed in M.P. Allen and D. Tildesley, Computer Simulation of Liquids (Oxford Univ. Press, Oxford, 1987).
7. K. Esselink, Large scale simulations of many particle systems, Ph.D. thesis, University of Groningen (1995).
8. J. Kolafa and J.W. Perram, Cutoff errors in the Ewald summation formula for point charge systems, Molec. Simulation 9 (1992) 351.
9. J.H. Ovesen, H.G. Petersen and J.W. Perram, Comparison of the minimum degree Cholesky method and the conjugate gradient method for molecular dynamics applications, to appear.
10. J.W. Perram, S.W. de Leeuw and H.G. Petersen, Hamilton's equations for constrained dynamical systems, J. Stat. Phys. 61 (1990) 1203-1222.
11. R. Edberg, D.J. Evans and G.P. Morriss, Constrained molecular dynamics: simulations of liquid alkanes with a new algorithm, J. Chem. Pys. 84 (1986) 6933-6939.
12. W. Joosen, S. Bijnens and P. Verbaeten, Object Parallelism in XENOOPS, Proc. 1st. Object-Oriented Numerics Conf., OONSKI'93, (1993).