On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

Journal of Computational Chemistry

Volumn 32, Issue 7, 2011, Pages 1228-1234

  Terakawa, Tsuyoshi ^a   Kameda, Tomoshi ^b   Takada, Shoji ^c  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

exchange; GROMACS; p53; protein; replica; REST

Indexed keywords

EXCHANGE; GROMACS; P53; REPLICA; REST;

AMINO ACIDS; PEPTIDES;

TEMPERING;

ALANINE; DIPEPTIDE;

ALGORITHM; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; SOLUBILITY;

ALANINE; ALGORITHMS; DIPEPTIDES; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; SOLUBILITY;

EID: 79953011717     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21703     Document Type: Article

References (31)

1. Swendsen, R.,;, Wang, J., Phys Rev Lett 1986, 57, 2607.
2. Hukushima, K.,;, Nemoto, K., J Phys Soc Jpn 1996, 65, 1604.
3. Sugita, Y.,;, Okamoto, Y., Chem Phys Lett 1999, 314, 141.
4. Mitsutake, A.,;, Sugita, Y.,;, Okamoto, Y., Biopolymers 2001, 60, 96.
5. Fukunishi, H.,;, Watanabe, O.,;, Takada, S., J Chem Phys 2002, 116, 9058.
6. Sugita, Y.,;, Okamoto, Y., Chem Phys Lett 2000, 329, 261.
7. Zhou, R., J Mol Graph Model 2004, 22, 451.
8. Liu, P.,;, Kim, B.,;, Friesner, R. A.,;, Berne, B. J., Proc Natl Acad Sci USA 2005, 102, 13749.
9. Kwak, W.,;, Hansmann, U., Phys Rev Lett 2005, 95, 138102.
10. Liu, P.,;, Huang, X.,;, Zhou, R.,;, Berne, B., J Phys Chem B 2006, 110, 19018.
11. Affentranger, R.,;, Tavernelli, I.,;, Di Iorio, E., J Chem Theory Comput 2006, 2, 217.
12. Okur, A.,;, Wickstrom, L.,;, Layten, M.,;, Geney, R.,;, Song, K.,;, Hornak, V.,;, Simmerling, C., J Chem Theory Comput 2006, 2, 420.
13. Huang, X.,;, Hagen, M.,;, Kim, B.,;, Friesner, R.,;, Zhou, R.,;, Berne, B., J Phys Chem B 2007, 111, 5405.
14. Hagen, M.,;, Kim, B.,;, Liu, P.,;, Friesner, R.,;, Berne, B., J Phys Chem B 2007, 111, 1416.
15. Babitzki, G.,;, Denschlag, R.,;, Tavan, P., J Phys Chem B 2009, 113, 10483.
16. Hukushima, K., Phys Rev E 1999, 60, 3606.
17. Sugita, Y.,;, Kitao, A.,;, Okamoto, Y., J Chem Phys 2000, 113, 6042.
18. Hess, B.,;, Kutzner, C.,;, van der Spoel, D.,;, Lindahl, E., J Chem Theory Comput 2008, 4, 435.
19. Duan, Y.,;, Wu, C.,;, Chowdhury, S.,;, Lee, M. C.,;, Xiong, G. M.,;, Zhang, W.,;, Yang, R.,;, Cieplak, P.,;, Luo, R.,;, Lee, T.,;, Caldwell, J.,;, Wang, J. M.,;, Kollman, P., J Comput Chem 2003, 24, 1999.
20. Jorgensen, W.,;, Chandrasekhar, J.,;, Madura, J.,;, Impey, R.,;, Klein, M., J Chem Phys 1983, 79, 926.
21. Essmann, U.,;, Perera, L.,;, Berkowitz, M. L.,;, Darden, T.,;, Lee, H.,;, Pedersen, L. G., J Chem Phys 1995, 103, 8577.
22. Hess, B., J Chem Theory Comput 2008, 4, 116.
23. Miyamoto, S.,;, Kollman, P., J Comput Chem 2004, 13, 952.
24. Nosé, S., Mol Phys 1984, 52, 255.
25. Hoover, W., Phys Rev A 1985, 31, 1695.
26. Patriksson, A.,;, Spoel, D., Phys Chem Chem Phys 2008, 10, 2073.
27. Jorgensen, W.,;, Maxwell, D.,;, Tirado-Rives, J., J Am Chem Soc 1996, 118, 11225.
28. Kaminski, G.,;, Friesner, R.,;, Tirado-Rives, J.,;, Jorgensen, W., J Phys Chem B 2001, 105, 6474.
29. Dawson, R.,;, Muller, L.,;, Dehner, A.,;, Klein, C.,;, Kessler, H.,;, Buchner, J., J Mol Biol 2003, 332, 1131.
30. Lee, H.,;, Mok, K.,;, Muhandiram, R.,;, Park, K.,;, Suk, J.,;, Kim, D.,;, Chang, J.,;, Sung, Y.,;, Choi, K.,;, Han, K., J Biol Chem 2000, 275, 29426.
31. Kussie, P.,;, Gorina, S.,;, Marechal, V.,;, Elenbaas, B.,;, Moreau, J.,;, Levine, A.,;, Pavletich, N., Science 1996, 274, 948.