DYNGA: A general purpose QM-MM-MD program. I. Application to water

Molecular Physics

Volumn 101, Issue 17, 2003, Pages 2659-2668

  Parker, Claudia L ^a   Ventura, Oscar N ^b   Burt, Stan K ^a   Cachau, Raúl E ^a,b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; COMPUTER SIMULATION; DIMERS; HAMILTONIANS; MOLECULAR DYNAMICS; PROTONS; WATER;

HYPERSURFACE; POLARIZABLE FORCE FIELDS; PROTON WIRES; WATER WATER INTERACTION;

MOLECULAR PHYSICS;

EID: 1542347882     PISSN: 00268976     EISSN: None     Source Type: Journal    
DOI: 10.1080/0026897031000137698     Document Type: Article

References (29)

1. Field, M. J., 2002, J. comput. Chem., 23, 48.
2. Amara, P., and Field, M. J., 1998, Encyclopedia of Computational Chemistry, edited by P. von Ragué Schleyer and P. R. Schreiner (New York: Wiley), p. 431.
3. Gao, J., 1998, Encyclopedia of Computational Chemistry, edited by P. von Ragué Schleyer, P. R. Schreiner, N. L. Allinger, T. Clark, J. Gasteiger and H. F. Schaefer III (New York: Wiley), p. 1257.
4. Merz Jr, K. M., and Stanton, R. V., 1998 Encyclopedia of Computational Chemistry, edited by P. von Ragué Schleyer, P. R. Schreiner, N. L. Allinger, T. Clark, J. Gasteiger and H. F. Schaefer III (New York: Wiley), p. 2330.
5. Sherwood, P., 2000, Modern Methods and Algorithms of Quantum Chemistry, edited by J. Grotendorst (Jülich: John von Neumann Institute for Computing), p. 257.
6. Schlegel, H. B., Millam, J. M., Iyengar, S. S., Voth, G. A., Daniels, A. D., Scuseria, G. E., and Frisch, M. J., 2001, Abstr. Pap. Am. chem. Soc., 222, 196.
7. Eichinger, M., Tavan, P., Hutter, J., and Parrinello, M., 1999, J. chem. Phys., 110, 10452.
8. Price, D. J., and Brooks III, C. L., 2002, J. comput. Chem., 23, 1045.
9. Jorgensen, W. L., and Tiradorives, J., 1988, J. Am. chem. Soc., 110, 1666.
10. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, A., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Stefánow, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gili, P. M. W., Johnson, B. G., Chen, W., Wong, M. W., Andress, J. L., Head-Gordon, M., Replgogle, E. S., and Pople, J. A., 1998, Gaussian'98 (Pittsburgh, PA: Gaussian, Inc.).
11. Brünger, A., 1993, X-PLOR Version 3.1 Manual (New Haven, CT: Yale University Press).
12. Foresman, J.B., and Frisch, A., 1995, Exploring Chemistry with Electronic Structure Methods (Pittsburgh, PA: Gaussian, Inc.).
13. Allen, M. P., and Tildesley, D. J., 1991, Computer Simulation of Liquids (Oxford: Clarendon Press).
14. Nosé, S., 1984, Molec. Phys., 52, 255.
15. Ciccotti, G., and Ryckakaert, J. P., 1986, Comput. Phys. Rep., 4, 345.
16. Wilson, W., 1984.
17. Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T., 1986, Numerical Recipes (Cambridge: Cambridge University Press).
18. Leach, A. R., 2001, Molecular Modelling, Principles and Applications (Harlow: Pearson Education Limited), pp. 618-619. 618-619.
19. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983, J. chem. Phys., 79, 926.
20. Oliphant, N., and Bartlett, R. J., 1994, J. chem. Phys., 100, 6550.
21. Binkley, J. S., Pople, J. A., and Hehre, W. J., 1980, J. Am. chem. Soc., 102, 939.
22. Ditchfield, R., Hehre, W. J., and Pople, J. A., 1971, J. chem. Phys., 54, 724.
23. Hehre, W. J., Ditchfield, R., and Pople, J. A., 1972, J. chem. Phys., 56, 2257.
24. Haharan, P. C., and Pople, J. A., 1973, Theoret. Chim. Acta, 28, 213.
25. Murphy, R. B., Philipp, D. M., and Friesner, R. A., 2000, J. comput. Chem., 21, 1442.
26. Delbene, J. E., Person, W. B., and Szczepaniak, K., 1995, J. phys. Chem., 99, 10705.
27. Freindorf, M., and Gao, J. L., 1996, J. comput. Chem., 17, 386.
28. Pomes, R., and Roux, B., 1998, Biophys. J., 75, 33.
29. Fraga, S., 1982, J. comput. Chem., 3, 329.