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Approach to thermal equilibrium in biomolecular simulation. (English) Zbl 1094.92004
Leimkuhler, Benedict (ed.) et al., New algorithms for macromolecular simulation. Selected papers based on the presentation at 4th international symposium, Leicester, UK, August 18–21, 2004. Berlin: Springer (ISBN 3-540-25542-7/pbk). Lecture Notes in Computational Science and Engineering 49, 125-140 (2006).
Summary: The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. 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.
For the entire collection see [Zbl 1084.81003].

MSC:
92C05 Biophysics
82D99 Applications of statistical mechanics to specific types of physical systems
92C40 Biochemistry, molecular biology
92-08 Computational methods for problems pertaining to biology
Software:
CHARMM
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