2010/04/12 by Y. Mori, Yoshiharu Mori, Mori, Yoshiharu +2 · 2 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · Physics and Astronomy · #Advanced Chemical Physics Studies #Algorithm #Canonical ensemble #Computer science #Constant (computer programming) #FOS: Physical sciences #Gaussian #Langevin dynamics #Mathematics #Molecular dynamics #Momentum (technical analysis) #Monte Carlo method #Physics #Protein Structure and Dynamics #Quantum mechanics #Replica #Spectroscopy and Quantum Chemical Studies #Statistical Mechanics (cond-mat.stat-mech) #Statistical physics #Thermodynamics #Thermostat #cond-mat.stat-mech
paper · pdf · doi:10.48550/arxiv.1004.2057
published in arXiv (Cornell University) (Cornell University) · 6 pages, (Revtex4), 4 figures
arxiv created 2010/04/12 · openalex publication_date 2010/04/12 · arxiv updated 2010/04/14 · openalex created_date 2019/06/27 · openalex updated_date 2026/07/28
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had previously been worked out only for the Gaussian constraint method. In this letter, we present momentum rescaling formulae for four other commonly used constant-temperature algorithms, namely, Langevin dynamics, Andersen algorithm, Nosé-Hoover thermostat, and Nosé-Poincaré thermostat. The effectiveness of these rescaling methods is tested with a small biomolecular system, and it is shown that proper momentum rescaling is necessary to obtain correct results in the canonical ensemble.