Approach to Thermal Equilibrium in Biomolecular Simulation
The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. In this paper, we study the way in which biomolecular systems achieve thermal equilibrium. In unthermostatted (constant energy) and Nosé-Hoover dynamics simulations, correct partition of energy is not observed on a typical MD simulation timescale. We discuss the practical use of numerical schemes based on Nosé-Hoover chains, Nosé-Poincaré and recursive multiple thermostats (RMT) , with particular reference to parameter selection, and show that RMT appears to show the most promise as a method for correct thermostatting. All of the MD simulations were carried out using a variation of the CHARMM package in which the Nosé-Poincaré, Nosé-Hoover Chains and RMT methods have been implemented.
KeywordsMolecular Dynamic Harmonic Oscillator Canonical Ensemble Average Kinetic Energy Symplectic Integrator
Unable to display preview. Download preview PDF.
- 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. 3586–3616Google Scholar
- S. Nosé, A molecular dynamics method for simulation in the canonical ensemble, Mol. Phys., 52, 255, 1984Google Scholar
- Dahlberg, Laaksonen and Leimkuhler, in preparationGoogle Scholar
- C.R. Sweet, Hamiltonian thermostatting techniques for molecular dynamics simulation, Ph.D. Dissertation, University of Leicester, 2004Google Scholar
- B. Laird, private communication.Google Scholar