Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics

Journal of Computational Chemistry

Volumn 27, Issue 14, 2006, Pages 1693-1702

  Lange, Oliver F ^a   Schäfer, Lars V ^a   Grubmüller, Helmut ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Chemical flooding; Conformational flooding; Enhanced sampling; Molecular dynamics; QM MM; Transition path prediction; Umbrella sampling

Indexed keywords

COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; COMPUTER SIMULATION; PROBLEM SOLVING; PROTEINS; REACTION KINETICS;

CHEMICAL FLOODING; CONFORMATIONAL FLOODING; ENHANCED SAMPLING; QM/MM; TRANSITION PATH PREDICTION; UMBRELLA SAMPLING;

MOLECULAR DYNAMICS;

BUTANE; CYCLOPROPANE DERIVATIVE;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; QUANTUM THEORY; TIME;

BUTANES; COMPUTER SIMULATION; CYCLOPROPANES; MODELS, CHEMICAL; QUANTUM THEORY; SOFTWARE; TIME FACTORS;

EID: 33748292739     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20473     Document Type: Article

References (37)

1. Karplus, M.; McCammon, J. A. Nat Struct Biol 2002, 9, 646.
2. de Groot, B. L.; Grubmüller, H. Curr Opin Struct Biol 2005, 15, 176.
3. Isralewitz, B.; Gao, M.; Schulten, K. Curr Opin Struct Biol 2001, 11, 224.
4. van Gunsteren,W. F.;Bakowies, D.; Baron, R.;Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glaettli, A.; Huenenberger, P. H.; Kastenholz, M. A.; Oostenbrink, C.; Schenk, M.; Trzesniak, D.; van der Vegt, N. F. A.; Yu, H. B. Angew Chem 2006, 45, 4064.
5. Grubmüller, H. Phys Rev E 1995, 52, 2893.
6. Tai, K. Biophys Chem 2004, 107, 213.
7. Schlegel, H. B. J Comput Chem 2003, 24, 1514.
8. Müller, E. M.; de Meijere, A.; Grubmüller, H. J Chem Phys 2002, 116, 897.
9. van der Spoel, D.; Hess, B.; Lindahl, E.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J Comput Chem 2005, 26, 1701.
10. Huber, T.; Torda, A. E.; van Gunsteren, W. F. J Comput Aided Mol Des 1994, 8, 695.
11. Voter, A. F. Phys Rev Lett 1997, 78, 3908.
12. Voter, A. F. J Chem Phys 1997, 106, 4665.
13. Hamelberg, D.; Mongan, J.; McCammon, J. A. J Chem Phys 2004, 120, 11919.
14. Laio, A.; Parrinello, M. Proc Natl Acad Sci USA 2002, 99, 12562.
15. Warshel, A.; Levitt, M. J Mol Biol 1976, 103, 227.
16. Kitao, A.; Hirata, F.; Go, N. Chem Phys 1991, 158, 447.
17. Garcia, A. E. Phys Rev Lett 1992, 68, 2696.
18. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins 1993, 17, 412.
19. Levitt, M.; Sander, C.; Stern, P. S. Int J Quantum Chem 1983, Suppl. 10, 181.
20. Brooks, B.; Karplus, M. Proc Natl Acad Sci USA, 1983, 80, 6571.
21. Go, N.; Noguti, T.; Nishikawa, T. Proc Natl Acad Sci USA, 1983, 80, 3696.
22. Amadei, A.; de Groot, B. L.; Ceruso, M. A.; Paci, M.; Nola, A. D.; Berendsen, H. J. C. Proteins: Struct Funct Genet 1999, 35, 283.
23. Hayward, S.; Kitao, A.; Hirata, F.; Go, N. J Mol Biol 1993, 234, 1207.
24. de Groot, B. L.; Vriend, G.; Berendsen, H. J. C. J Mol Biol 1999, 286, 1241.
25. Groenhof, G.; Bouxin-Cademartory, M.; Hess, B.; de Visser, S. P.; Berendsen, H. J. C.; Olivucci, M.; Mark, A. E.; Robb, M. A. J Am Chem Soc 2004, 126, 4228.
26. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.: Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li. X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian, Inc.: Wallingford, CT, 2004.
27. Vollhardt. K. P.; Schore, N. E. Organic Chemistry. W H Freeman: New York, 1998.
28. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
29. Miyamoto, S.; Kollman, P. A. J Comp Chem 1992, 13, 952.
30. Nendel, M.; Sperling, D.; Wiest, O.; Houk, K. N. J Org Chem 2000, 65, 3259.
31. Engels, B.; Hanrath, M.; Lennartz, C. Computers and Chemistry 2001, 25, 15.
32. Nakamura, E.; Yamago, S.; Ejiri, S.; Dorigo, A. E.; Morokuma, K. J Am Chem Soc 1991, 113, 3183.
33. Hess, B. Phys Rev E 2002, 65, 031910.
34. Faraldo-Gomez, J. D.; Forrest, L. R.; Baaden, M.; Bond, P. J.; Domene, C.; Patargias, G.; Cuthbertson, J.; Sansom, M. S. P. Proteins 2004, 57, 783.
35. Baisera, M. A.; Wriggers,W.; Oono, Y.; Schulten, K. J Phys Chem 1996, 100, 2567.
36. Torrie, G. M.; Valle, J. P. J Comput Phys 1977, 23, 187.
37. Souaille, M.; Roux, B. Comput Phys Commun 2001, 135, 40.