A multicanonical ab initio molecular dynamics method: Application to conformation sampling of alanine tripeptide

Chemical Physics Letters

Volumn 432, Issue 1-3, 2006, Pages 306-312

  Jono, Ryota ^a   Shimizu, Kentaro ^a   Terada, Tohru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; CONFORMATIONS; FREE ENERGY; MOLECULAR DYNAMICS; SAMPLING;

ALANINE PEPTIDE; ATOMIC CHARGES; CLASSICAL SIMULATIONS; FREE-ENERGY LANDSCAPES;

PROTEINS;

EID: 33750949602     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2006.10.080     Document Type: Article

References (32)

1. Karplus M., and McCammon J.A. Nat. Struct. Biol. 9 (2002) 646
2. Hansson T., Oostenbrink C., and van Gunsteren W.F. Curr. Opin. Struct. Biol. 12 (2002) 190
3. Leforestier C. J. Chem. Phys. 68 (1978) 4406
4. Car R., and Parrinello M. Phys. Rev. Lett. 55 (1985) 2471
5. Marx D., and Hutter J. In: Grotendorst J. (Ed). Modern Methods and Algorithms of Quantum Chemistry. second ed. NIC Series vol. 3 (2000), John von Neumann Institute for Computing, Jülich 329
6. Berg B.A., and Neuhaus T. Phys. Lett. B 267 (1991) 249
7. Berg B.A., and Neuhaus T. Phys. Rev. Lett. 68 (1992) 9
8. Hukushima K., and Nemoto K. J. Phys. Soc. Jpn. 65 (1996) 1604
9. Zhu Z., Tuckerman M.E., Samuelson S.O., and Martyna G.J. Phys. Rev. Lett. 88 (2002) 100201
10. Laio A., and Parrinello M. Proc. Natl. Acad. Sci. USA 99 (2002) 12562
11. Hansmann U.H.E., Okamoto Y., and Eisenmenger F. Chem. Phys. Lett. 259 (1996) 321
12. Nakajima N., Nakamura H., and Kidera A. J. Phys. Chem. B 101 (1997) 817
13. Sugita Y., and Okamoto Y. Chem. Phys. Lett. 314 (1999) 141
14. Mitsutake M., Sugita Y., and Okamoto Y. Biopolymers (Pept. Sci.) 60 (2001) 96
15. Ishitani R., Shimizu K., and Terada T. J. Chem. Phys. 124 (2006) 214902
16. Ensing B., Vivo M.D., Liu Z., Moore P., and Klein M.L. Acc. Chem. Res. 39 (2006) 73
17. Iannuzzi M., Laio A., and Parrinello M. Phys. Rev. Lett. 90 (2003) 238302
18. Frisch M.J., et al. Gaussian 03, Revision C.02 (2004), Gaussian, Inc.,, Wallingford CT
19. Schmidt M.W., et al. J. Comput. Chem. 14 (1993) 1347
20. Binkley J.S., Pople J.A., and Hehre W.J. J. Am. Chem. Soc. 102 (1980) 939
21. Evans D.J., Hoover W.G., Failor B.H., Moran B., and Ladd A.J.C. Phys. Rev. A 28 (1983) 1016
22. Zhang F. J. Chem. Phys. 106 (1997) 6102
23. Ferrenberg A.M., and Swendsen R.H. Phys. Rev. Lett. 61 (1988) 2635
24. Terada T., Matsuo Y., and Kidera A. J. Chem. Phys. 118 (2003) 4306
25. Case D.A., Pearlman D.A., Caldwell J.W., Cheatham T.E., Ross W.S., Simmerling C.L., Darden T.A., Merz K.M., Stanton R.V., Cheng A.L., Vincent J.J., Crowley M., Tsui V., Radmer R.J., Duan Y., Pitera J., Massova I., Sibel G.L., Singh U.C., Weiner P.K., and Kollman P.A. Amber 6 (1999), University of California, San Francisco
26. Wang J., Cieplak P., and Kollman P.A. J. Comput. Chem. 21 (2000) 1049
27. Simmerling C., Strockbine B., and Roitberg A.E. J. Am. Chem. Soc. 124 (2002) 11258
28. Head-Gordon T., Head-Gordon M., Frisch M.J., Brooks III C.L., and Pople J.A. J. Am. Chem. Soc. 113 (1991) 5989
29. Venkatachalam C.M. Biopolymers 6 (1968) 1425
30. Beachy M.D., Chasman D., Murphy R.B., Halgren T.A., and Friesner R.A. J. Am. Chem. Soc. 119 (1997) 5908
31. Breneman C.M., and Wiberg K.B. J. Comput. Chem. 11 (1990) 361
32. Halgren T.A., and Damm W. Curr. Opin. Struct. Biol. 11 (2001) 236