On the performance of molecular dynamics applications on current high-end systems
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[1] Martyn F. Guest. Application Performance on High-End and Commodity-class computers , 2003 .
[2] P. M. Rodger,et al. DL_POLY: Application to molecular simulation , 2002 .
[3] R W Hockney,et al. Computer Simulation Using Particles , 1966 .
[4] Laxmikant V. Kalé,et al. NAMD: Biomolecular Simulation on Thousands of Processors , 2002, ACM/IEEE SC 2002 Conference (SC'02).
[5] D. J. Tildesley,et al. Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm , 1991 .
[6] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[7] D. C. Rapaport,et al. Multi-million particle molecular dynamics: II. Design considerations for distributed processing , 1991 .
[8] Laxmikant V. Kalé,et al. CHARM++: a portable concurrent object oriented system based on C++ , 1993, OOPSLA '93.
[9] W Smith,et al. DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.
[10] I T Todorov,et al. DL_POLY_3: the CCP5 national UK code for molecular–dynamics simulations , 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.
[11] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[12] Stephen Booth,et al. HPCx: towards capability computing , 2005, Concurr. Pract. Exp..
[13] Laxmikant V. Kale,et al. NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .
[14] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[15] D. C. Rapaport,et al. Multi-million particle molecular dynamics I. Design considerations for vector processing , 1991 .
[16] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[17] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[18] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[20] Steve Plimpton,et al. Fast parallel algorithms for short-range molecular dynamics , 1993 .