Bad seeds sprout perilous dynamics: Stochastic thermostat induced trajectory synchronization in biomolecules

Journal of Chemical Theory and Computation

Volumn 5, Issue 6, 2009, Pages 1624-1631

  Sindhikara, Daniel J ^a   Kim, Seonah ^b   Voter, Arthur F ^c   Roitberg, Adrian E ^a  

^a University of Florida   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 67650072432     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct800573m     Document Type: Article

References (35)

1. Tuckerman, M. E.; Martyna, G. J. Understanding modern molecular dynamics: Techniques and applications. J. Phys. Chem. B 2000, 104 (2), 159-178.
2. Berendsen, H. J. C.; Potsma, J. P. M.; van Gunsteren, W. F.; DiNola, A. D.; Haak, J. R. Molecular Dynamics with Coupling to and External Bath. J. Chem. Phys. 1984, 81, 3684-3690.
3. Nose, S. A Molecular-Dynamics Method for Simulations in the Canonical Ensemble. Mol. Phys. 1984, 52 (2), 255-268.
4. Hoover, W. G. Canonical Dynamics - Equilibrium Phase- Space Distributions. Phys. Rev.A 1985, 31 (3), 1695-1697.
5. Evans, D. J.; Holian, B. L. The Nose-Hoover Thermostat. J. Chem. Phys. 1985, 83 (8), 4069-4074.
6. Andersen, H. C. Molecular-Dynamics Simulations at Constant Pressure and-or Temperature. J. Chem. Phys. 1980, 72 (4), 2384-2393.
7. Zwanzig, R. Nonlinear generalized Langevin equations. J Stat. Phys. 1973, 9 (3), 215-220.
8. Andersen, H. C. Molecular Dynamics at Constant Pressure and/or Temperature. J. Chem. Phys. 1980, 72, 2384.
9. Hunenberger, P. Thermostat algorithms for molecular dynamics simulations. In Advanced Computer Simulation Approaches for Soft Matter Sciences I; Springer: Berlin/ Heidelberg, 2005; Vol. 173, pp 105-147.
10. Braxenthaler, M.; Unger, R.; Auerbach, D.; Given, J. A.; Moult, J. Chaos in protein dynamics. Proteins: Struct., Funct., Genet. 1997, 29 (4), 417-425.
11. Uberuaga, B. P.; Anghel, M.; Voter, A. F. Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. J Chem. Phys 2004, 120 (14), 6363-6374.
12. Le Jan, Y. Equilibre statistique pour les produits de difféomorphismes aléatoires indépendants. Annales de l'l.H.P. Probabilités et statistiques 1987, 23 (1), 111-120.
13. Fahy, S.; Hamann, D. R. Transition from Chaotic to Nonchaotic Behavior in Randomly Driven Systems. Phys. Rev. Lett. 1992, 69 (5), 761-764.
14. Maritan, A.; Banavar, J. R. Chaos, Noise, and Synchronization. Phys. Rev. Lett. 1994, 72 (10), 1451-1454.
15. Lise, S.; Maritan, A.; Swift, M. R. Langevin equations coupled through correlated noises. J. Phys. A: Math. Gen. 1999, 32 (28), 5251-5260.
16. Ciesla, M.; Dias, S. P.; Longa, L.; Oliveira, F. A. Synchronization induced by Langevin dynamics. Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2001, 6306 (6), -.
17. Longa, L.; Curado, E. M. F.; Oliveira, F. A. Roundoff-induced coalescence of chaotic trajectories. Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 1996, 54 (3), R2201-R2204.
18. Cerutti, D. S.; Duke, R.; Freddolino, P. L.; Fan, H.; Lybrand, T. P. A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. J. Chem. Theory Comput. 2008, 4, 1669-1680.
19. Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314 (1-2), 141-151.
20. Hansmann, U. H. E. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 1997, 281 (1-3), 140-150.
21. Hagen, M.; Kim, B.; Liu, P.; Friesner, R. A.; Berne, B. J. Serial replica exchange. J. Phys. Chem. B 2007, 111 (6), 1416-1423.
22. Shen, H. J.; Czaplewski, C.; Liwo, A.; Scheraga, H. A. Implementation of a serial Replica Exchange Method in a physics-based united-residue (UNRES) force field. J Chem Theory Comput.. 2008, 4 (8), 1386-1400.
23. Rick, S. W. Replica exchange with dynamical scaling. J. Chem. Phys. 2007, 126 (5), 054102.
24. Okamoto, Y. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graphics Modell. 2004, 22 (5), 425-439.
25. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26 (16), 1668-1688.
26. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple amber force fields and development of improved protein backbone
27. parameters. Proteins: Struct.. Fund... Rioinf. 2006, 65 (3), 712-725.
28. Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Struct.. Funct.. Rioinf. 2004, 55 (2), 383-394.
29. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical- Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23 (3), 327-341.
30. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graphics Modell. 1996, 14 (1), 33-&.
31. Friedberg, R.; Cameron, J. E. Test of Monte-Carlo Method - Fast Simulation of a Small Ising Lattice. J. Chem. Phys. 1970, 52 (12), 6049-6058.
32. Wang, T.; Du, D. G.; Gai, F. Helix-coil kinetics of two 14-residue peptides. Chem.. Phys. Lett. 2003, 370 (5- 6), 842-848.
33. Kim, S.; Roitberg, A. E. Simulating temperature jumps for protein folding. J. Phys. Chem.. B 2008, 112 (5), 1525-1532.
34. Sreerama, N.; Woody, R. W., Computation and analysis of protein circular dichroism spectra. Methods Enzymol 2004, 383, 318-351.
35. Marsaglia, G.; Narasimhan, B.; Zaman, A. A Random Number Generator for Pcs. Comput. Phys. Commun. 1990, 60 (3), 345-349.