Constant temperature constrained molecular dynamics: The Newton-Euler inverse mass operator method

Journal of Physical Chemistry

Volumn 100, Issue 25, 1996, Pages 10508-10517

  Vaidehi, Nagarajan ^a   Jain, Abhinandan ^b   Goddard III, William A ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0003864349     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp953043o     Document Type: Article

References (27)

1. Mazur, A.; Abagayan, R. J. Biomol. Struct. Dyn. 1989, 6, 815.
2. Jain, A.; Vaidehi, N.; Rodriguez, G. J. Comput. Phys. 1993, 106, 258.
3. Rice, L. M.; Brunger, A. T. Proteins: Struct., Funct., Genet. 1994, 19, 277.
4. Mathiowetz, A.; Jain, A.; Karasawa, N.; Goddard, W. A., III. Proteins: Struct., Funct., Genet. 1994, 20, 227.
5. See also: Mathiowetz, A. Ph.D. Thesis, Department of Chemistry, California Institute of Technology, 1992.
6. Ding, H. Q.; Karasawa, N.; Goddard, W. A., III. J. Chem. Phys. 1992, 97, 4309.
7. Nosé, S. J. Chem. Phys. 1984, 81, 511.
8. Hoover, W. G. Phys. Rev. 1985, A31, 1695.
9. Hoover, W. G. Computational Statistical Mechanics; Elsvier: Amsterdam, 1991.
10. Rodriguez, G.; Jain, A.; Kreutz-Delgado, K. J. Astronaut. Sci. 1992, 40, 27.
11. Rodriguez, G. IEEE J. Rob. Automat. 1987, 3, 624.
12. The NEIMO-Hoover calculations were carried out using POLYGRAF (from Materials Simulations Incorporated, Burlington, MA) modified to include the NEIMO option. All the polyethylene and amorphous PVC simulations were done with DREIDING FF.
13. Nosé, S. Prog. Theor. Phys. Suppl. 1991, 103, 1.
14. Ashurst, W. T.; Hoover, W. G. Phys. Rev. Lett. 1973, 31, 206.
15. Woodcock, L. V. Chem. Phys. Lett. 1971, 10, 257.
16. Abraham, F. F.; Koch, S. W.; Desai, R. C. Phys. Rev. Lett. 1983, 78, 2626.
17. Haile, S.; Gupta, S. J. Chem. Phys. 1983, 79, 3067.
18. Andersen, H. C. J. Chem. Phys. 1980, 72, 2384.
19. Nosé, S. Mol. Phys. 1984, 52, 255.
20. Cagin, T.; Goddard, W. A., III; Ary, M. L. Comput. Polym. Sci. 1991, 1, 241.
21. DiTolla, F. D.; Ronchetti, M. Phys. Rev. E 1993, 48, 1726.
22. Cho, K.; Joannopoulos, J. D. Phys. Rev. A 1992, 45, 7089.
23. Karasawa, N.; Dasgupta, S.; Goddard, W. A., III. J. Phys. Chem. 1991, 95, 2260.
24. 24 FF and conjugate gradient minimization. The charge on H is 0.1440. A spline cutoff radius of 9 A was used to calculate the nonbond forces with the inner and outer match radii being 8 and 8.5 Å, respectively. The nonbond pair list was updated every 0.1 ps of the simulation.
25. Mayo, S. I.; Olafson, B. D.; Goddard, W. A., III. J. Phys. Chem. 1990, 94, 8897.
26. Karasawa, N.; Goddard, W. A., III. Macromolecules 1992, 25, 7268.
27. Karasawa, N.; Goddard, W. A., III. J. Phys. Chem. 1989, 93, 7320.