Comparative Molecular Dynamics and Monte Carlo Study of Statistical Properties for Coarse-Grained Heteropolymers

Details Comparative Molecular Dynamics and Monte Carlo Study of Statistical Properties for Coarse-Grained Heteropolymers Comparative Molecular Dynamics and Monte Carlo Study of Statistical Properties for Coarse-Grained Heteropolymers

2009-02-11

arxiv.org/abs/0902.1918v1

J. Comput. Chem. 29, 2603-2612 (2008)

Physics

Condensed Matter

Statistical Mechanics

37 pages, 8 figures, 2 tables

Scientific paper

Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nose-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nose-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of the Nose-Hoover chain thermostat. Autocorrelations from molecular dynamics and Metropolis Monte Carlo runs are also investigated.

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