Approach to Thermal Equilibrium in Biomolecular Simulation

Eric Barth, Ben Leimkuhler, Chris Sweet

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract / Description of output

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.

Original languageEnglish
Title of host publicationNew Algorithms for Macromolecular Simulation
PublisherSpringer-Verlag
Pages125-140
Number of pages16
ISBN (Print)9783540255420
DOIs
Publication statusPublished - 2006

Publication series

NameLecture Notes in Computational Science and Engineering
Volume49
ISSN (Print)1439-7358

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