Discontinuous molecular dynamics for rigid bodies: Applications

Journal of Chemical Physics

Volumn 126, Issue 7, 2007, Pages

  Hernández De La Peña, Lisandro ^a   Van Zon, Ramses ^a   Schofield, Jeremy ^a   Opps, Sheldon B ^b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF PRINCE EDWARD ISLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; COMPUTER SIMULATION; MATHEMATICAL MODELS; METHANE; MOLECULAR PHYSICS;

LENNARD JONES POTENTIALS; MOLECULAR MASS DISTRIBUTIONS; RIGID BODY SYSTEMS;

MOLECULAR DYNAMICS;

EID: 33847242925     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2434959     Document Type: Article

References (20)

1. B. J. Alder and T. E. J. Wainwright, J. Chem. Phys. 31, 459 (1959).
2. D. C. Rapaport, J. Chem. Phys. 71, 3299 (1979).
3. A. Bellemans, J. Orban, and D. VanBelle, Mol. Phys. 39, 781 (1980).
4. G. A. Chapela, S. E. Martínez-Casas, and J. Alejandre, Mol. Phys. 53, 139 (1984).
5. G. A. Chapela, H. T. Davis, and L. E. Sciven, Chem. Phys. 129, 201 (1989).
6. Y. Zhou and M. Karplus, J. Mol. Biol. 293, 917 (1999).
7. F. Ding, J. M. Borreguero, S. V. Buldyrey, H. E. Stanley, and N. V. Dokholyan, Proteins: Struct., Funct., Genet. 53, 220 (2003).
8. H. D. Nguyen and C. K. Hall, J. Am. Chem. Soc. 128, 1890 (2006).
9. R. van Zon and J. Schofield, e-print cond-mat/0612404.
10. L. Hernández de la Peña, R. van Zon, J. Schofield, and S. B. Opps, J. Chem. Phys. 126, 074105 (2007), preceding paper.
11. A. Dullweber, B. Leimkuhler, and R. McLachlan, J. Chem. Phys. 107, 5840 (1997).
12. Such initial conditions can be found using a hybrid Monte Carlo method [see, e.g., S. Duane, A. D. Kennedy, B. J. Pendleton, and D. Roweth, Phys. Lett. B 195, 216 (1987)], which can be realized within the context of simulating rigid bodies, since the dynamics in these simulations is time reversible and area preserving, being derived from a Hamiltonian.
13. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran; The Art of Scientific Computing, 2nd ed. (Cambridge University Press, Cambridge, 1992).
14. D. C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, Cambridge, 2004).
15. A. D. MacKerell, Jr., D. Bashford, M. Bellott, J. Phys. Chem. B 102, 3586 (1998).
16. R. van Zon and J. Schofield, J. Comput. Phys. (in press).
17. C. De Michele, S. Gabrielli, P. Tartaglia, and F. Sciortino, J. Phys. Chem. B 110, 8064 (2006).
18. N. Zacharopoulos, N. Vergadou, and D. N. Theodorou, J. Chem. Phys. 122, 244111 (2005).
19. D. R. Falcone, D. C. Douglass, and D. W. McCall, J. Ceram. Soc. Jpn. 71, 2754 (1967).
20. I. Cacelli, G. Cinacchi, G. Prampolini, and A. Tani, J. Am. Chem. Soc. 126, 14278 (2004).