Approach to Thermal Equilibrium in Biomolecular Simulation

Lecture Notes in Computational Science and Engineering

Volumn 49, Issue , 2006, Pages 125-140

  Barth, Eric ^a   Leimkuhler, Ben ^b   Sweet, Chris ^b  

^a KALAMAZOO COLLEGE   (United States)

^b UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUMERICAL METHODS; THERMODYNAMICS;

BIOMOLECULAR SIMULATION; BIOMOLECULAR SYSTEM; DYNAMICS SIMULATION; MOLECULAR-DYNAMICS MODEL; NUMERICAL SCHEME; PARAMETER SELECTION; TEMPERATURE CONTROL METHODS; THERMAL EQUILIBRIUMS;

MOLECULAR DYNAMICS;

EID: 35348925007     PISSN: 14397358     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-31618-3_8     Document Type: Article

References (18)

1. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan and M. Karplus, CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comp. Chem, 4 (1983), pp. 187-217
2. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher III, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin and M. Karplus, An all-atom empirical potential for molecular modeling and dynamics of proteins, J. Phys. Chem., 102 (1998), pp. 3586-3616
3. S. Jang and G. Voth, Simple reversible molecular dynamics algorithms for Nosé-Hoover chain dynamics, J. Chem. Phys. 110: 3263 (1999)
4. S.D. Bond, B.B. Laird and B. J. Leimkuhler, The Nosé-Poincaré method for constant temperature molecular dynamics, J. Comp. Phys., 151, 114, 1999
5. S. Nosé, A molecular dynamics method for simulation in the canonical ensemble, Mol. Phys., 52, 255, 1984
6. Yi Liu and Mark E. Tuckerman, Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble, J. Chem. Phys, 112, 1685-1700, 2000
7. W. G. Hoover, Canonical dynamics: equilibrium phase-space distributions, Phys. Rev. A 31, 1695 (1985)
8. B. J. Leimkuhler and C. R. Sweet, Hamiltonian formulation for recursive multiple thermostats in a common timescale, SIADS, 4, No. 1, pp. 187-216, 2005
9. B.B. Laird and J.B. Sturgeon, Symplectic algorithm for constant-pressure molecular dynamics using a Nosé-Poincaré thermostat, J. Chem. Phys., 112, 3474, 2000
10. Hernandez, E. Metric-tensor flexible-cell algorithm for isothermal-isobaric molecular dynamics simulations. J. Chem. Phys., 115, 10282-10291, 2001
11. Dahlberg, Laaksonen and Leimkuhler, in preparation
12. G.J. Martyna, M.L. Klein and M. Tuckerman, Nosé-Hoover chains: The canonical ensemble via continuous dynamics, J. Chem. Phys., 97, 2635, 1992
13. B.J. Leimkuhler and C.R. Sweet, The canonical ensemble via symplectic integrators using Nosé and Nosé-Poincaré chains, J. Chem. Phys., 121, 1, 2004
14. B.B. Laird and B.J. Leimkuhler, A generalized dynamical thermostatting technique, Phys. Rev. E, 68, 16704, 2003
15. S. Nosé, An improved symplectic integrator for Nosé-Poincaré thermostat, J. Phys. Soc. Jpn, 70, 75, 2001
16. C.P. Dettmann, Hamiltonian for a restricted isoenergetic thermostat, Phys. Rev. E, 60, 7576, 1999
17. C.R. Sweet, Hamiltonian thermostatting techniques for molecular dynamics simulation, Ph.D. Dissertation, University of Leicester, 2004
18. B. Laird, Private communication.