The Performance of Different Communication Mechanisms and Algorithms Used for Parallelization of Molecular Dynamics Code

1. S. T. Wlodek, Terry Clark, L. Ridgway Scott, and J. Andrew McCammon. Molecular dynamics of Acetylcholinesterase dimer complexed with Tacrine. Journal of the American Chemical Society, 119(40):9513–952, 1997.

   Article  Google Scholar 

2. T. W. Clark and J. A. McCammon. Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. Computers & Chemistry, 14(3):219–24, 1990.

   Article  Google Scholar 

3. T. Clark, R. von Hanxleden, J. A. McCammon, and L. R. Scott. Parallelizing molecular dynamics using spatial decomposition. In Scalable High Performance Computing Conference, pages 95–102, Knoxville, TN, May 1994. IEEE Computer Society. Available via anonymous ftp from softlib.rice.eduaspub/CRPC-TRs/reports/CRPC-TR93356-S

   Google Scholar 

4. S. Plimpton. Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117:1–19, March 1995.

   Google Scholar 

5. T. Clark, R. von Hanxleden, K. Kennedy, C. Koelbel, and L. R. Scott. Evaluating parallel languages for molecular dynamics computations. In Scalable High Performance Computing Conference, Williamsburg, VA, 1992. IEEE. Available via anonymous ftp from oftlib.rice.edu as pub/CRPC-TRs/reports/CRPC-TR992202-S.

   Google Scholar 

6. R. von Hanxleden. Compiler Support for Machine-Independent Parallelization of Irregular Problems. PhD thesis, Rice University, December 1994. Available via anonymous ftp from softlib.rice.edu as pub/CRPC-TRs/reports/CRPC-TR94495-S.

   Google Scholar 

7. P. Bała, T. W. Clark, and L. R. Scott. Application of Pfortran and Co-Array fortran in the parallelization of the GROMOS96 molecular dynamics module. In M. Bubak, J. Moűciñski, and Marian Noga, editors, SGI Users’ Conference-Conference Processdings, pages 194–204. Academic Computer Centre CYFRONET AGH, 2000.

   Google Scholar 

8. P. Bała, T. W. Clark, and L. R. Scott. Application of Pfortran and Co-Array fortran in the parallelization of the GROMOS96 molecular dynamics module. Su-percomputing Journal 2001 (in press)

   Google Scholar 

9. W. Van Gunsteren and H. J. C. Berendsen. GROMOS (Groningen Molecular Simulation Computer Program Package). Biomos, Laboratory of Physical Chemistry, ETH Zentrum, Zurich, 1996.

   Google Scholar 

10. B. Bagheri, T. W. Clark, and L. R. Scott. Pfortran: a parallel dialect of fortran. ACM Fortran Forum, 11(3):20–31, 1992.

    Article  Google Scholar 

11. M. P. Allen and D. J. Tildesley. Computer simulations of liquids. Clarendon, Oxford, 1987.

    Google Scholar 

12. W. F. van Gunsteren and H. J. C. Berendsen. A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3):173–182, 1988.

    Article  Google Scholar 

13. W. F. van Gunsteren and H. J. C. Berendsen. Algorithms for brownian dynamics. Molecular Physics, 45:637–647, 1982.

    Article  Google Scholar 

14. J. W. Eastwood R. W. Hockney. Computer Simulation Using Particles. Cambridge University Press, Cambridge, 1987.

    Google Scholar 

15. USA NERSC, Lawrance Research Laboratory. MVICH-MPI for virtual interface architecture. http://www.nersc.gov/research/FTG/mvich, 2000.

16. USA NERSC, Lawrance Research Laboratory. M-VIA: A high performance modular via for linux. http://www.nersc.gov/research/FTG/via, 2000.

17. R. W. Numrich. F^—: a parallel extension to Cray fortran. Scientific Programming, 6(3):275–84, 1997.

    Google Scholar 

18. R. W. Numrich, J. Reid, and K. Kim. Writing a multigrid solver using Co-Array fortran. In B. Kågström, J. Dongarra, E. Elmroth, and J. Waśniewski, editors, Recent Advances in Applied Parallel Computing, Lecture Notes in Computer Science 1541, pages 390–399. Springer-Verlag Berlin, 1998.

    Google Scholar 

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