Implementation of the replica-exchange molecular dynamics method for rigid bodies

International Journal of Quantum Chemistry

Volumn 106, Issue 10, 2006, Pages 2208-2213

  Moskovsky, A A ^a,b   Vanovschi, V V ^a   Konyukhov, S S ^a   Nemukhin, A V ^a,b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b EMANUEL INSTITUTE OF BIOCHEMICAL PHYSICS   (Russian Federation)

Author keywords

Distributed calculations; Geometry optimization; QM MM methods; Replica exchange molecular dynamics (REMD); Rigid body molecular dynamics

Indexed keywords

COMPUTER SYSTEMS PROGRAMMING; CONFORMATIONS; OPTIMIZATION; PROTEINS; QUANTUM THEORY; THERMOSTATS;

DISTRIBUTED CALCULATIONS; GEOMETRY OPTIMIZATION; QM/MM METHODS; REPLICA-EXCHANGE MOLECULAR DYNAMICS (REMD); RIGID-BODY MOLECULAR DYNAMICS;

MOLECULAR DYNAMICS;

EID: 33745797711     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.20940     Document Type: Article

References (29)

1. Warshel, A.; Levitt, M. J Mol Biol 1976, 103, 227.
2. Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Burt, S. K. J Phys Chem A 2002, 106, 10663.
3. Nemukhin, A. V.; Grigorenko, B. L.; Bochenkova, A. V.; Topol, I. A.; Burt, S. K. J Mol Struct (Theochem) 2002, 581, 167.
4. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K. J Comp Chem 2003, 24, 1410.
5. Nemukhin, A. V.; Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K. Theor Chem Acc 2004, 111, 36.
6. Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Cachau, R. E.; Burt, S. K. Proteins 2005, 60, 495.
7. Granovsky, A. URL http://lcc.chem.msu.ru/gran/gamess/index.html.
8. 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., Jr. J Comput Chem 1993, 14, 1347.
9. Sugita, Y.; Okamoto, Y. Chem Phys Lett 1999, 314, 141.
10. Gullingsrud, J. URL http://www.ks.uiuc.edu/Developments/MDTools/mindy.
11. Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J Comp Phys 1999, 151, 283.
12. Brooks, B.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
13. Dullweber, A.; Leimukhler, B.; McMachlan, R. J Chem Phys 1997, 107, 5840.
14. Martyna, G. J.; Klein, M. L.; Tuckerman, M. J Chem Phys 1992, 97, 2635.
15. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J Chem Phys 1994, 101, 4177.
16. Garcia, A. E.; Sanbonmatsu, K. Y. Proteins 2001, 42, 345.
17. Zhou, R.; Berne, B. J.; Germain, R. Proc Natl Acad Sci USA 2001, 98, 14931.
18. Garcia, A. E.; Sanbonmatsu, K. Y. Proc Natl Acad Sci USA 2002, 99, 2782.
19. Rhee, Y. M.; Pande, V. S. Biophys J 2003, 84, 775.
20. Pitera, J. W.; Swope, W. Proc Natl Acad Sci USA 2003, 100, 7587.
21. Garcia, A. E.; Onuchic, J. N. Proc Natl Acad Sci USA 2003, 100, 13898.
22. Rao, F.; Caflish, A. J Chem Phys 2003, 119, 4035.
23. Cecchini, M.; Rao, F.; Seeber, M.; Caflish, A. J Chem Phys 2004, 121, 10748.
24. Paschek, D.; Garcia, A. Phys Rev Lett 2004, 93, 238105.
25. Nguyen, P. N.; Mu, Y.; Stock, G. Proteins 2005, 60, 485.
26. Abramov, S. M.; Adamovich A. I. URL http://www.botik.ru/~abram/ts-pubs. html.
27. Abramov, S. M.; Adamovich, A. I.; Inyukhin, A. V.; Moskovsky, A. A.; Roganov, A. V.; Shevchuk, E. V. In Proceedings of the Conference on Supercomputing Systems and Applications; Belarus: Minsk, 2004.
28. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem. Phys 1983, 79, 926.
29. Wales, D. J.; Hodges, M. P. Chem Phys Lett 1998, 286, 65.