Abstract
Thermostats are dynamical equations used to model thermodynamic variables such as temperature and pressure in molecular simulations. For computationally intensive problems such as the simulation of biomolecules, we propose to average over fast momentum degrees of freedom and construct thermostat equations in configuration space. The equations of motion are deterministic analogues of the Smoluchowski dynamics in the method of stochastic differential equations.
Similar content being viewed by others
References
Peyrard, M.: Nonlinearity 17, R1 (2004)
Morriss, G.P., Dettmann, C.P.: Chaos 8, 321 (1998)
Tuckerman, M.E., Martyna, G.J.: J. Phys. Chem. B 104, 159 (2000)
Kusnezov, D., Bulgac, A., Bauer, W.: Ann. Phys. 204, 155 (1990)
Hoover, Wm.G., Aoki, K., Hoover, C.G., De Groot, S.V.: Physica D 187, 253 (2004)
Hoover, Wm.G.: Mol. Simul. 33, 13 (2007)
Gardiner, C.W.: Handbook of Stochastic Methods. Springer, Berlin (2004)
Kramers, H.A.: Physica 7, 284 (1940)
Samoletov, A.A.: J. Stat. Phys. 96, 1351 (1999)
Rugh, H.H.: Phys. Rev. Lett. 78, 772 (1997)
Jepps, O.G., Ayton, G., Evans, D.J.: Phys. Rev. E 62, 4757 (2000)
Hamilton, I.P.: Phys. Rev. A 42, 7467 (1990)
L’Heureux, I., Hamilton, I.: Phys. Rev. E 47, 1411 (1993)
Samoletov, A., Chaplain, M.: Fiz. Tekhnika Vysok. Davl. 15, 61 (2005) (in Russian)
Martyna, G.J., Klein, M.L., Tuckerman, M.: J. Chem. Phys. 97, 2635 (1992)
Braga, C., Travis, K.P.: J. Chem. Phys. 123, 134101 (2005)
Samoletov, A., Chaplain, M., Dettmann, C.: arXiv/physics/0412163 (2004)
Dettmann, C.P., Morriss, G.P.: Phys. Rev. E 55, 3693 (1997)
Landau, L.D., Lifshitz, E.M.: Mechanics. Pergamon, London (1959)
Landau, L.D., Lifshitz, E.M.: Statistical Physics. Pergamon, New York (1976)
Gallavotti, G.: Statistical Mechanics. Springer, Berlin (1999)
Gihman, I.I., Skorohod, A.V.: Stochastic Differential Equations. Springer, Berlin (1972)
Delhommelle, J.: Phys. Rev. B 69, 144117 (2004)
Delhommelle, J., Petravic, J., Evans, D.J.: J. Chem. Phys. 120, 6117 (2004)
Katok, A., Hasselblatt, B.: Modern Theory of Dynamical Systems. Cambridge University Press, Cambridge (1995)
Lang, S.: Introduction to Differentiable Manifolds. Springer, Berlin (2002)
Branka, A.C.: Phys. Rev. E 61, 4769 (2000)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Samoletov, A.A., Dettmann, C.P. & Chaplain, M.A.J. Thermostats for “Slow” Configurational Modes. J Stat Phys 128, 1321–1336 (2007). https://doi.org/10.1007/s10955-007-9365-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10955-007-9365-2