Grid-flux method for learning the solvent contribution to the mechanisms of reactions

Journal of Physical Chemistry B

Volumn 107, Issue 12, 2003, Pages 2796-2801

  McCormick, Thomas A ^a   Chandler, David ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DIPEPTIDE; ATOMIC POSITIONS; GRID FLUX METHOD; MOMENTA;

COMPUTER SIMULATION; CRYSTAL ATOMIC STRUCTURE; DATA REDUCTION; DISSOCIATION; FLUXES; ISOMERIZATION; MOLECULAR DYNAMICS; SODIUM CHLORIDE; SOLVENTS;

REACTION KINETICS;

EID: 0038394215     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp027290l     Document Type: Article

References (11)

1. Frenkel, D.; Smit, B. In Understanding Molecular Simulation; Academic Press Inc.: San Diego, 2002.
2. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. Annu. Rev. Phys. Chem. 2002, 59, 291.
3. Bolhuis, P. G.; Dellago, C.; Chandler, D. Proc. Natl. Acad. Sci. 2000, 97, 5877.
4. Geissler, P. L.; Dellago, C.; Chandler, D. J. Phys. Chem. B 1999, 103, 3706.
5. The flux calculations require only that each of the configurations of the system along each trajectory be transformed to a common coordinate system and that any motions of the solvent molecules between cells in the spatial grid be recorded as fluxes.
6. Pettit, B. M.; Rossky, P. J. J. Chem. Phys. 1986, 84, 5836.
7. Jorgenson, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
8. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L., et.al. AMBER 5; University of California, San Francisco, 1997.
9. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D. M.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1.
10. Goldberg, D. E. In Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley: Reading, MA, 1993.
11. Devijver, P. A.; Kittler, J. Pattern Recognition: A Statistical Approach; Prentice Hall: London, 1982.