A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations

Journal of Computational Chemistry

Volumn 22, Issue 5, 2001, Pages 501-508

  Kräutler, Vincent ^a   Van Gunsteren, Wilfred F ^a   Hünenberger, Philippe H ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Constraints; Molecular dynamics; SHAKE procedure

Indexed keywords

EID: 0035871686     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V     Document Type: Article

References (20)

1. van Gunsteren, W. F.; Berendsen, H. J. C. Mol Phys 1977, 34, 1311.
2. van Gunsteren, W. F. Mol Phys 1980, 40, 1015.
3. van Gunsteren, W. F.; Karplus, M. Macromolecules 1982, 15, 1528.
4. Tironi, I. G.; Brunne, R. M.; van Gunsteren, W. F. Chem Phys Lett 1996, 250, 19.
5. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
6. Miyamoto, S.; Kollman, P. A. J Comput Chem 1992, 13, 952.
7. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J Comput Chem 1997, 18, 1463.
8. Andersen, H. C. J Comput Phys 1983, 52, 24.
9. Hockney, R. W.; Eastwood, J. W. Computer Simulation Using Particles; Institute of Physics Publishing: Bristol, 1981.
10. Golub, G. H.; van Loan, C. F. Matrix Computations; Johns Hopkins University Press: London, 1996.
11. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel, Dordrecht: The Netherlands, 1981, p. 331.
12. Liu, H.; Müller-Plathe, F.; van Gunsteren, W. F. J Am Chem Soc 1995, 117, 4363.
13. Tironi, I. G.; van Gunsteren, W. F. Mol Phys 1994, 83, 381.
14. Dietz, W.; Heinzinger, K. Ber Bunsenges Chem 1984, 88, 543.
15. Dietz, W.; Heinzinger, K. Ber Bunsenges Chem 1985, 89, 968.
16. Barker, J. A.; Watts, R. O. Mol Phys 1973, 26, 789.
17. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1995, 102, 5451.
18. Berendsen, H. J. C; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
19. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Verlag der Fachvereine: Zürich, 1996.
20. Pearlman, D. A.; Case, D. A.; Caldwell, J. D.; Ross, W. S.; Cheatham, T. E., III; DeBolt, S.; Fergusson, D.; Seibel, G.; Kollman, P. Comput Phys Commun 1995, 91, 1.