An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations

Journal of Chemical Physics

Volumn 122, Issue 14, 2005, Pages

  Christen, Markus ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BOND-LENGTH VIBRATIONS; FLEXIBLE CONSTRAINTS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SYSTEMS;

ALGORITHMS; APPROXIMATION THEORY; COMPUTER SIMULATION; CONSTRAINT THEORY; HAMILTONIANS; KINETIC ENERGY; LAGRANGE MULTIPLIERS; MOLECULAR VIBRATIONS; MONTE CARLO METHODS; POTENTIAL ENERGY;

MOLECULAR DYNAMICS;

EID: 20844441640     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1872792     Document Type: Article

References (24)

1. M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids (Oxford Science, Oxford, 1987).
2. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
3. K. A. Feenstra, B. Hess, and H. J. C. Berendsen, J. Comput. Chem. 20, 786 (1999).
4. G. Ciccotti, M. Ferrario, and J.-P. Ryckaert, Mol. Phys. 47, 1253 (1982).
5. H. C. Andersen, J. Comput. Phys. 52, 24 (1983).
6. S. Miyamoto and P. A. Kollman, J. Comput. Chem. 13, 952 (1992).
7. V. Kräutler, W. F. van Gunsteren, and P. H. Hünenberger, J. Comput. Chem. 22, 501 (2001).
8. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys. 47, 721 (1982).
9. D. M. Ferguson, J. Comput. Chem. 16, 501 (1995).
10. D. A. Doyle, J. M. Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbis, S. L. Cohen, B. T. Chait, and R. MacKinnon, Science 280, 69 (1998).
11. D. Meuser, H. Splitt, R. Wagner, and H. Schrempf, FEBS Lett. 462, 447 (1999).
12. K. Toukan and A. Rahman, Phys. Rev. B 31, 2643 (1985).
13. J. Anderson, J. J. Ullo, and S. Yip, J. Chem. Phys. 87, 1726 (1987).
14. L. X. Dang and B. M. Pettitt, J. Chem. Phys. 86, 6560 (1987).
15. O. Teleman, B. Joensson, and S. Engstrom, Mol. Phys. 60, 193 (1987).
16. G. Corongiu, Int. J. Quantum Chem. 42, 1209 (1992).
17. I. G. Tironi, R. M. Brunne, and W. F. van Gunsteren, Chem. Phys. Lett. 250, 19 (1996).
18. P. J. van Maaren and D. van der Spoel, J. Phys. Chem. B 105, 2618 (2001).
19. J. Zhou, S. Reich, and B. R. Brooks, J. Chem. Phys. 112, 1919 (2000).
20. B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002).
21. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulberlag AG an der ETH Zürich, Zürich, Switzerland.
22. W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, J. Phys. Chem. A 103, 3596 (1999).
23. L. D. Schuler, X. Daura, and W. F. van Gunsteren, J. Comput. Chem. 22, 1205 (2001).
24. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).