ORAC: A molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions

Journal of Computational Chemistry

Volumn 18, Issue 15, 1997, Pages 1848-1862

  Procacci, Piero ^a,d   Darden, Tom A ^b   Paci, Emanuele ^c,e   Marchi, Massimo ^c  

^a UNIVERSITÉ DE LYON   (France)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c DSV   (France)

^d UNIVERSITY OF FLORENCE   (Italy)

^e UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Biomolecules; Electrostatics; Molecular dynamics; Reversible multiple time step algorithms; Software

Indexed keywords

EID: 0010262629     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O     Document Type: Article

References (52)

1. A. Rahman, Phys. Rev., 136, 405 (1964).
2. L. Verlet, Phys. Rev., 159, 98 (1967).
3. M. E. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys., 97, 1990 (1992).
4. D. D. Humphreys, R. A. Friesner, and B. J. Berne, J. Phys. Chem., 98, 6885 (1994).
5. M. Watanabe and M. Karplus, J. Phys. Chem., 99, 5680 (1995).
6. P. Procacci and B. J. Berne, J. Chem. Phys., 1015, 2421 (1994).
7. P. Procacci and M. Marchi, J. Chem. Phys., 104, 3003 (1996).
8. L. Greengard and V. Rokhlin, J. Comput. Phys., 73, 325 (1987).
9. K. E. Schmidt and M. A. Lee, J. Stat. Phys., 63, 1223 (1991).
10. T. Darden, D. York, and L. Pedersen, J. Chem. Phys., 98, 10089 (1993).
11. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys., 101, 8577 (1995).
12. P. Procacci, T. Darden, and M. Marchi, J. Phys. Chem., 100, 10464 (1996).
13. H. Berendsen, Molecular Dynamics and Protein Structure, Polycrystal Book Service, Western Spring, IL, 1985.
14. H. Lee, T. A. Darden, and L. G. Pedersen, J. Chem. Phys., 102, 3830 (1995).
15. M. Saito, J. Chem. Phys., 101, 4055 (1994).
16. P. Procacci and B. J. Berne, Mol. Phys., 83, 255 (1994).
17. H. C. Andersen, J. Chem. Phys., 72, 2384 (1980).
18. M. Parrinello and A. Rahman, Phys. Rev. Lett., 45, 1196 (1980).
19. S. Nosè, J. Chem. Phys., 81, 511 (1984).
20. B. R. Brooks, R. E. Bruccoeri, B. D. Olafson, D. J. States, S. Swaminanthan, and M. Karplus, J. Comput. Chem., 4, 187 (1983).
21. S. J. Wiener, P. A. Kollmann, D. T. Nguyen, and D. A. Case, J. Comput. Chem. 7, 230 (1986).
22. W. D. Cornell, P. Cieplak, C. I. Bavly, I. R. Gould, K. M. Merz Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. Kollmann, J. Am. Chem. Soc., 117, 5179 (1995).
23. G. Ciccotti, M. Ferrario, and J.-P. Ryckaert, Mol. Phys., 47, 1253 (1982).
24. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys., 79, 926 (1983).
25. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Oxford University Press, Oxford, 1989.
26. P. Ewald, Ann. Phys., 64, 253 (1921).
27. S. W. deLeeuw, J. W. Perram, and E. R. Smith, Proc. R. Soc. Lond. A, 373, 27 (1980).
28. P. E. Smith and B. M. Pettitt, J. Chem. Phys., 105, 4289 (1996).
29. R. W. Hockney, Computer Simulation Using Particles, McGraw-Hill, New York, 1989
30. H. C. Petersen, J. Chem. Phys., 103, 3668 (1995).
31. M. E. Tuckerman and B. J. Berne, J. Chem. Phys., 95, 8362 (1991).
32. M. E. Tuckerman, G. J. Martyna, and B. J. Berne, J. Chem. Phys., 94, 6811 (1991).
33. M. E. Tuckerman, B. J. Berne, and A. Rossi, J. Chem. Phys., 94, 1465 (1990).
34. Polygen Corp. Parameter and Topology files for CHARMm, Version 22 (copyright 1986, release 1992)
35. M. E. Tuckerman and M. Parrinello, J. Chem. Phys., 101, 1302 (1994).
36. M. E. Tuckerman and M. Parrinello, J. Chem. Phys., 101, 1316 (1994).
37. H. de Raedt and B. de Raedt, Phys. Rev. A, 28, 3575 (1983).
38. H. Goldstein, Classical Mechanics, Addison-Wesley, Reading, MA, 1980.
39. S. K. Grey, J. Chem. Phys., 101, 4062, 1994.
40. E. Paci and M. Marchi, J. Phys. Chem., 104, 3003 (1996).
41. M. Ferrario and J.-P. Ryckaert, Mol. Phys., 78, 7368 (1985).
42. S. Nosé, Prog. Theor. Phys., 103(Suppl.), 1 (1991).
43. M. Ferrario, Computer Simulation in Chemical Physics, M. P. Allen and D. J. Tildesley, Eds., Kluwer, Dordrecht, 1993.
44. C. Ciccotti and J.-P. Ryckaert, Computer Phys. Rep., 4, 345 (1986).
45. G. L. Martyna, M. L. Klein, and M. Tuckerman, J. Chem. Phys., 97, 2635 (1992)
46. J.-P. Ryckaert and G. Ciccotti, J. Chem. Phys., 78, 7368 (1983).
47. S. Nosé and M. L. Klein, Mol. Phys., 50, 1055 (1983).
48. M. Marchi and P. Procacci, ORAC Manual and Guide, CECAM-ENS, Lyon 1997 (available at ftp.cecam.fr:/pub/orac/doc/manual.ps).
49. J. J. P. Stewart, J. Comput. Chem., 10, 221 (1989).
50. S. J. Weiner, P. A. Kollmann, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta Jr., and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984).
51. S. Parkin, B. Rupp, and H. Hope, The structure of bovine pancreatic trypsin inhibitor at 125k: Definition of carboxyl-terminal residues glycine-57 and alanine-58 (manuscript submitted).
52. G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, Mol. Phys., 87, 1117 (1996).