Chapter

New Algorithms for Macromolecular Simulation

Volume 49 of the series Lecture Notes in Computational Science and Engineering pp 125-140

Approach to Thermal Equilibrium in Biomolecular Simulation

  • Eric BarthAffiliated withDepartment of Mathematics, Kalamazoo College
  • , Ben LeimkuhlerAffiliated withCentre for Mathematical Modelling, University of Leicester
  • , Chris SweetAffiliated withCentre for Mathematical Modelling, University of Leicester

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Abstract

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.