Approach to Thermal Equilibrium in Biomolecular Simulation

  • Eric Barth
  • Ben Leimkuhler
  • Chris Sweet
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 49)


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) [8], 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.


Molecular Dynamic Harmonic Oscillator Canonical Ensemble Average Kinetic Energy Symplectic Integrator 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Eric Barth
    • 1
  • Ben Leimkuhler
    • 2
  • Chris Sweet
    • 2
  1. 1.Department of MathematicsKalamazoo CollegeKalamazooUSA
  2. 2.Centre for Mathematical ModellingUniversity of LeicesterLeicesterUK

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