|
|
|
|
References
|
|
| |
| 1. |
D. Frankel, B. Smith, Understanding molecular simulations, Second edition, Academic press, New York, 2002, 658 pp. |
| 2. |
K. Esselink, B. Smit, P. A. Hilbers, “Efficient parallel implementation of molecular dynamics on a toroidal
network: I. Parallelizing strategy”, J. Comp. Phys., 106 (1993), 101–107   |
| 3. |
G. S. Grest, B. Dunweg, K. Kremer, “Vectorized link cell Fortran code for molecular dynamics simulations
for large number of particles”, Comp. Phys. Comm., 55 (1989), 269–285 |
| 4. |
S. Plimpton, “Fast parallel Algorithms for Short-Range Molecular Dynamics”, J. of computational physics, 117 (1995), 1–19  |
| 5. |
H. J. C. Berendsen, D. van der Spoel, R. van Drunen, “GROMACS: A message-passing parallel molecular dynamics implementation”, Comp. Phys. Comm., 91 (1995), 43–56 |
| 6. |
P. Alexander Lyubartsev, Aatto Laaksonen, “M. DynaMix – a scalable portable parallel MD simulation package
for arbitrary molecular mixtures”, Computer Physics Communications, 128 (2000), 565–589 |
| 7. |
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa,
C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, “Scalable molecular dynamics with NAMD”, J. Comp. Chem., 26:16 (2005), 1781–1802 |
| 8. |
A. F. Bakker, G. H. Glimer, M. H. Grabow, K. Thompson, “A special purpose computer for molecular dynamics calculations”, J. Comp. Phys., 90 (1990), 313–335  |
| 9. |
Ryutaro Susukita, Toshikazu Ebisuzaki, Bruce G. Elmegreen,
Hideaki Furusawa, Kenya Kato, Atsushi Kawai, Yoshinao Kobayashi,
Takahiro Koishi, Geoffrey D. McNiven, Tetsu Narumi, Kenji Yasuoka, “Hardware accelerator for molecular dynamics: MDGRAPE-2”, Computer Physics Communications, 155 (2003), 115–131 |
| 10. |
Randima Fernando, Mark J. Kilgard, The Cg Tutorial. The Definitive Guide to Programmable Real-Time
Graphics, Addison Wesley Professional, 2003 |
| 11. |
NVIDIA. CUDA Programming Guide Version 1.0, 2006 |
| 12. |
Juekuan Yang, Yujuan Wang, Yunfei Chen, “GPU accelerated molecular dynamics simulation of thermal conductivities”, J. of Computational Physics, 221 (2007), 799–804 |
| 13. |
J. A. van Meel, A. Arnold, D. Frenkel, S. F. P. Zwart, R. G. Belleman, Harvesting graphics power for MD simulations, arxiv: org.0709.3225v1[cond-mat.other] |
| 14. |
Joshua A. Anderson, Chris D. Lorenz, A. Travesset, “General Purpose Molecular Dynamics Simulations Fully Implemented
on Graphics Processing Units”, J. of Computational Physics, 227:10 (2008), 5342–5359 |
| 15. |
J. E. Stone, J. C. Phillips, P. L. Freddolino, D. J. Hardy,
L. G. Trabuco, K. Schulten, “Accelerating molecular modeling applications with graphics processors”, J. Comp. Chem., 28 (2007), 2618–2640 |
| 16. |
U. Burker, N. L. Allinger, Molecular Mechanics, ACS Monograph, 177, 1982 |
| 17. |
D. W. Cornell, P. Cieplak, I. B. Christopher, I. R. Gould,
M. M. Kenneth, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell,
P. A. Kollman, “A Second Generation Force Field for the Simulation of Proteins,
Nucleic Acids, and Organic Molecules”, J. Am. Chem. Soc., 117 (1995), 5179–5197 |
| 18. |
TINKER – Software Tools for Molecular Design, http://dasher.wustl.edu/tinker/ |
| 19. |
HyperCube, Inc., HyperChem Computational Chemistry, Publication HC70-00-04-00, 2002 |
