Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations

Journal of Computational Chemistry

Volumn 30, Issue 12, 2009, Pages 1799-1815

  Queyroy, Séverine ^a,b   Nakamura, Haruki ^c   Fukuda, Ikuo ^d,e  

^a FUJITSU LABORATORIES LTD   (Japan)

^b AIX MARSEILLE UNIVERSITY   (France)

^c OSAKA UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

Author keywords

Extended phase space; Molecular dynamics; Nos Hoover equations; Ordinary differential equation; Volume preserving integrator

Indexed keywords

COMPUTATIONAL COSTS; CONSTANT TEMPERATURE MOLECULAR DYNAMICS; DIVERGENCE FREE; EQUATION PARAMETER; EXTENDED PHASE SPACE; EXTENDED VERSIONS; HIGHER ORDER; INITIAL VALUES; LIQUID ARGON; LIQUID WATER; MOLECULAR DYNAMICS SIMULATIONS; NUMERICAL EXAMINATION; NUMERICAL INTEGRATOR; PHASE SPACES; PHASE-SPACE VOLUME; TIME INVARIANTS; TIME STEP LENGTH; VOLUME PRESERVING INTEGRATOR; VOLUME-PRESERVING INTEGRATORS;

AMINES; ARGON; BOUNDARY CONDITIONS; DYNAMICAL SYSTEMS; DYNAMICS; LIQUEFIED GASES; MOLECULAR DYNAMICS;

ORDINARY DIFFERENTIAL EQUATIONS;

ALANYLALANINE; ARGON; DIPEPTIDE; WATER;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; TEMPERATURE;

ALGORITHMS; ARGON; COMPUTER SIMULATION; DIPEPTIDES; MODELS, MOLECULAR; TEMPERATURE; WATER;

EID: 68549109418     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21181     Document Type: Article

References (39)

1. Fukuda, I.; Nakamura, H. Phys Rev E 2006, 73, 026703.
2. Ruth, R. D. IEEE Trans Nucl Sci 1983, NS-30, 2669.
3. Yoshida, H. Phys Lett A 1990, 150, 262.
4. McLachlan, R. I.; Atela, P. Nonlinearity 1992, 5, 541.
5. Okunbor, D. I. J Comput Phys 1995, 120, 375.
6. Quispel, G. R. W.; Dyt, C. P. Phys Lett A 1998, 242, 25.
7. Morrison, P. J. Rev Mod Phys 1998, 70, 467.
8. Nosé, S. Mol Phys 1984, 52, 255.
9. Hoover, W. G. Phys Rev A 1985, 31, 1695.
10. Hoover, W. G.; Holian, B. L. Phys Lett A 1996, 211, 253.
11. Martyna, G. J.; Klein, M. L.; Tuckermann, M. J Chem Phys 1992, 97, 2635.
12. Kuznesov, D.; Bulgac, A.; Bauer, W. Ann Phys 1990, 204, 155.
13. Hoover, W. G. Phys Rev A 1986, 34, 2499.
14. Stern, H. A. J Comput Chem 2004, 25, 749.
15. Gear, C. W. Numerical Intitial Value Problems in Ordinary Differential Equations; Prentice-Hall: Englewood Cliffs, 1971.
16. Bond, S.; Laird, B.; Leimkuhler, B. J Comput Phys 1999, 151, 114.
17. Berendsen, H. J. C.; Postma, J. P. M.; Gunsteren, W. F. van; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
18. Hamilton, I. P. Phys Rev A 1990, 42, 7467.
19. Sergi, A.; Ferrario, M. Phys Rev E 2001, 64, 056125.
20. Ramshaw J. D. Europhys Lett 2002, 59, 319.
21. Evans, D. J.; Morriss, G. P. Statistical Mechanics of Non-Equilibrium Liquids; Academic: London, 1990.
22. Hoover, W. G. Time Reversibility, Computer Simulation, and Chaos; World Scientific: Singapore, 2001.
23. McLachlan, R. I. SIAM J Sci Comput 1995, 16, 151.
24. Hairer, E.; Lubitch, C.; Wanner, G. Geometric Numerical Integration; Springer-Verlag: Berlin, 2002.
25. Blanes, S.; Moan, P. C. J Comput Appl Math 2002, 142, 313.
26. Cano, B.; Sanz-Serna, J. M. SIAM J Numer Anal 1997, 34, 1391.
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
28. Okunbor, D. I.; Skeel, R. D. J Comp Chem 1994, 15, 72.
29. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
30. Ishida, H.; Kidera, A. J Chem Phys 1998, 109, 3276.
31. McLachlan, R. I.; Quispel, G. R. W. J Phys A: Math Gen 2006, 39, 5251.
32. Fukuda, I.; Nakamura, H. J Phys Chem B 2004, 108, 4162.
33. Schlick, T.; Mandziuk, M.; Skeel, R. D.; Srinivas, K. J Comp Phys 1998, 140, 1.
34. Mandziuk, M.; Schlick, T. Chem Phys Lett 1995, 237, 525.
35. Batcho, P. F.; Schlick, T. J Chem Phys 2001, 115, 4019.
36. Garcia-Archilla, B.; Sanz-Serna, J. M.; Skeel, R. D. SIAM J Sci Comp 1998, 20, 930.
37. Fukuda, I.; Queyroy, S.; Nakamura, H. in preparation.
38. Aoki, K.; Kusnezov, D. Phys Lett A 265, 2000, 250.
39. Venneri, G. D.; Hoover, W. G. J Comput Phys 1987, 73, 468. Journal of Computational Chemistry DOI 10.1002/jcc