First-principle molecular dynamics with ultrasoft pseudopotentials: Parallel implementation and application to extended bioinorganic systems

Journal of Chemical Physics

Volumn 120, Issue 13, 2004, Pages 5903-5915

  Giannozzi, P ^a,b   De Angelis, F ^a,c   Car, R ^a  

^a PRINCETON UNIVERSITY   (United States)

^b INFM   (Italy)

^c UNIVERSITY OF PERUGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINORGANIC SYSTEMS; VALENCE ELECTRONS;

BIOCATALYSTS; CARRIER CONCENTRATION; ELECTROSTATICS; FAST FOURIER TRANSFORMS; INTEGRAL EQUATIONS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; ORGANOMETALLICS; PROTEINS;

ELECTRONIC STRUCTURE;

IRON; MANGANESE; METALLOPORPHYRIN; MYOGLOBIN;

ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; CONFORMATION; METABOLISM; THERMODYNAMICS;

BINDING SITES; COMPUTATIONAL BIOLOGY; IRON; MANGANESE; METALLOPORPHYRINS; MOLECULAR CONFORMATION; MYOGLOBIN; THERMODYNAMICS;

EID: 1942470906     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1652017     Document Type: Review

References (37)

1. P. Hohenberg and W. Kohn, Phys. Rev. 136, B864 (1964).
2. W. Kohn and L. J. Sham, Phys. Rev. 140, A1133 (1965).
3. R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985).
4. D. R. Hamann, M. Schlüter, and C. Chiang, Phys. Rev. Lett. 43, 1494 (1979).
5. L. J. Clarke, I. Ştich, and M. C. Payne, Comput. Phys. Commun. 72, 14 (1993).
6. D. Marx and J. Hutter, in Modern Methods and Algorithms of Quantum Chemistry (John von Neumann Institute for Computing, FZ Jülich, 2000), pp. 301-449.
7. C. Cavazzoni and G. L. Chiarotti, Comput. Phys. Commun. 123, 56 (1999).
8. D. Vanderbilt, Phys. Rev. B 41, 7892 (1990).
9. P. E. Blöchl, Phys. Rev. B 50, 17953 (1994).
10. B. Hetényi, F. De Angelis, P. Giannozzi, and R. Car, J. Chem. Phys. 115, 5791 (2001).
11. K. Laasonen, A. Pasquarello, R. Car, C. Lee, and D. Vanderbilt, Phys. Rev. B 47, 10142 (1993).
12. G. Makov and M. C. Payne, Phys. Rev. B 51, 4014 (1995).
13. P. Pulay, Mol. Phys. 17, 197 (1969).
14. F. Tassone, F. Mauri, and R. Car, Phys. Rev. B 50, 10561 (1994).
15. R. Car and M. Parrinello, in Simple Molecular Systems at Very High Density (Plenum, New York, 1989), p. 455.
16. S. de Gironcoli (private communication).
17. Message Passing Interface Forum: MPI: A message-passing interface standard, Int. J. Supercomput. Appl. 8, 3/4 (1994).
18. A large collection of highly optimized libraries for linear algebra can be found at the URL (http://www.netlib.org)
19. C. Rovira, K. Kunc, J. Hutter, P. Ballone, and M. Parrinello, J. Phys. Chem. A 101, 8914 (1997).
20. S. E. V. Phillips and B. P. Schoenborn, Nature (London) 292, 81 (1981).
21. A. D. Becke, J. Chem. Phys. 84, 4524 (1986).
22. J. P. Perdew, Phys. Rev. B 33, 8822 (1986).
23. J. P. Perdew, J. A. Chevary, S. H. Vosko, K. A. Jackson, D. J. Singh, and C. Fiolhais, Phys. Rev. B 46, 6671 (1992).
24. Code CP, available at the URL 〈http://www.democritos.it/scientific. php〉
25. N. Troullier and J. L. Martins, Phys. Rev. B 46, 1754 (1992).
26. A computer code for US-PP generation can be downloaded at the URL 〈http://www.physics.rutgers.edu/~dhv/uspp/〉
27. J. N. Harvey, J. Am. Chem. Soc. 123, 142 (2001).
28. R. W. Hockney and J. W. Eastwood, in Computer Simulation Using Particles (McGraw-Hill, New York, 1981), p. 211.
29. G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. 110, 2810 (1999).
30. N. Jin and J. T. Groves, J. Am. Chem. Soc. 121, 2923 (1999).
31. N. Jin, J. L. Bourassa, S. Tizio, and J. T. Groves, Angew. Chem., Int. Ed. Engl. 39, 3849 (2000).
32. T. Ziegler, V. Tshinke, E. J. Baerends, J. G. Snijders, and W. Ravenek, J. Phys. Chem. 93, 3050 (1989).
33. E. J. Baerends, D. E. Ellis, and P. Ros, Chem. Phys. 2, 42 (1973).
34. E. J. Baerends and P. Ros, Chem. Phys. 2, 51 (1973).
35. E. J. Baerends and P. Ros, Chem. Phys. 8, 41 (1975).
36. E. J. Baerends and P. Ros, Int. J. Quantum Chem. S12, 169 (1978).
37. ADF STO's basis set database is available at the URL 〈http://tc. chem.vu.nl/SCM/Doc/atomicdatabase〉