An efficient real space multigrid QM/MM electrostatic coupling

Journal of Chemical Theory and Computation

Volumn 1, Issue 6, 2005, Pages 1176-1184

  Laino, Teodoro ^a,b   Mohamed, Fawzi ^b   Laio, Alessandro ^b   Parrinello, Michele ^b  

^a SCUOLA NORMALE SUPERIORE   (Italy)

^b ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33646205963     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct050123f     Document Type: Article

References (47)

1. Freely available at the URL: http://cp2k.berlios.de, released under GPL license.
2. Head-Gordon, M. J. Phys. Chem. 1996, 100, 13213-13225.
3. York, D.; Lee, T.; Yang, W. Phys. Rev. Lett. 1998, 80, 5011.
4. Soler, J. M.; Artacho E.; Gale J. D.; Garcia A.; Junquera J.; Ordejon P.; Sanchez-Portal D. J. Phys.: Condens. Matter 2002, 14, 2745-2779.
5. Gogonea, V.; Merz, K. M. J. Phys. Chem. A 1999, 103, 5171.
6. Scuseria, G. E. J. Phys. Chem. A 1999, 103, 4782.
7. Greatbanks, S. P.; Gready, J. E.; Limaye, A. C.; Rendell, A. P. J. Comput. Chem. 2000, 21, 788.
8. Khandogin, J.; York, M. D. J. Phys. Chem. B 2002, 106, 7693.
9. Krajewski, F.; Parrinello, M. Phys. Rev. B 2005, 71 (23), Art. No. 233105.
10. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249.
11. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1986, 7, 718-730.
12. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733.
13. Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170-1179.
14. Crespo, A.; Scherlis, D. A.; Martí, M. A.; Ordejon, P.; Roitberg, A. E.; Estrin, D. A. J. Phys. Chem. B 2003, 107, 13728-13736.
15. Thompson, M. A. J. Phys. Chem. 1995, 99, 4794-4804.
16. Yarne, D. A.; Tuckerman, M. E.; Martyna, G. J. J. Chem. Phys. 2001, 115, 3531-3539.
17. Laio, A.; VandeVondele, J.; Rothlisberger, U. J. Chem. Phys. 2002, 116, 6941-6947.
18. Nam, K.; Gao, J.; York, D. M. J. Chem. Th. Comput. 2005, 1, 2-13.
19. Lyne, P. D.; Hodoscek, M.; Karplus, M. J. Phys. Chem. A 1999, 103, 3462-3471.
20. Field, M. J.; Albe, M.; Bret, C.; Proust-De Martin, F.; Thomas, A. J. Comput. Chem. 2000, 21, 1088-1100.
21. Sherwood, P.; de Vries, A. H.; Guest, M. F.; Schreckenbach, G.; Catlow, C. R. A.; French S. A.; Sokol, A. A.; Bromley, S. T.; Thiel, W.; Turner, A. J.; Billeter, S.; Terstegen, F.; Thiel, S.; Kendrick, J.; Rogers, S. C.; Casci, J.; Watson, M.; King, F.; Karlsen, E.; Sjøvoll, M.; Fahmi, A.; Schäfer, A.; Lennartz, C. J. Mol. Struct. (THEOCHEM) 2003, 632, 1-28
22. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. A.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902.
23. Ferre, N.; Olivucci, M. J. Am. Chem. Soc. 2003, 125, 6868-6869.
24. Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M. J. Chem. Phys. 1999, 110, 10452-10467.
25. Loferer, M. J.; Loeffler, H. H.; Liedl, K. R. J. Commit. Chem. 2003, 24, 1240-1249.
26. Karlström, G.; Lindh, R.; Malmqvist, P.-A.; Roos, B. O.; Ryde, U.; Veryazov, V.; Widmark, P.-O.; Cossi, M.; Schim-melpfennig, B.; Neogrady, P.; Seijo, L. Commit. Mater. Sci. 2003, 28, 222.
27. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347-1363.
28. Hutter, J.; Alavi, A.; Deutsch, T.; Ballone, P.; Bernasconi, M.; Focher, P.; Fois, E.; Goedecker, S.; Marx, D.; Parrinello, M.; Tuckerman, M. CPMD V.9.1; Technical Report; MPI fur Festkörperforschung, Stuttgart and IBM: Zurich Research Laboratory, 2005.
29. Fusti-Molnar, L.; Pulay, P. J. Chem. Phys. 2002, 116, 7795-7805.
30. Sherwood, P. In Modern Methods and Algorithms of Quantum Chemistry; John von Neumann Institute for Computing: 2000; Chapter Hybrid quantum mechanics/molecular mechanics approaches, Vol. 1, pp 257-277.
31. VandeVondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Comm. 2005, 167, 103-128.
32. Kohn, W.; Sham, L. Phys. Rev. 1965, 140, A1133-A1138.
33. Density Functional Theory of Atoms and Molecules; Oxford University Press: New York, 1989.
34. Lippert, G.; Hutter, J.; Parrinello, M. Theor. Chem. Acc. 1999, 103, 124-140.
35. Lee, Y.; Hodoscek, M.; Brooks, B.; Kador, P. Biophys. Chem. 1998, 70, 203-216.
36. Case, D.; et al. AMBER V.7.0; Technical Report; University of California: San Francisco, 2002.
37. Amara, P.; Field M. J. Theor. Chem. Acc. 2003, 109, 43-52
38. Das, D.; Eurenius, P. K.; Billings, E. M.; Sherwood, P.; Chatfield, C. D.; Hodoscek, M.; Brooks, B. R. J. Chem. Phys. 2002, 117, 10534-10547
39. The Mathematica Notebook used to develop the GEEP technology is part of the CP2K distribution and can be freely downloaded. Released under GPL license.
40. Multi-Grid Methods and Applications; Springer-Verlag: Berlin, 1985; Vol. 4 of Series in Computational Mathematics.
41. A Multigrid Tutorial; SIAM Books: Philadelphia, PA, 1987.
42. Feng, G. IEEE Trans. Signal Process. 1998, 46, 2790-2796.
43. Pulay, P. Mol. Phys. 1969, 17, 197.
44. Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981; Chapter Interaction models for water in relation to protein hydration, pp 331-342.
45. Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. B 1996, 54, 1703-1710.
46. Becke, A. D. Phys. Rev. A 1988, 38, 3098.
47. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.