Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms

2010/04/12 by Y. Mori, Mori, Yoshiharu, Yuko Okamoto +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced Chemical Physics Studies #FOS: Physical sciences #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #Statistical Mechanics (cond-mat.stat-mech)

paper · pdf · doi:10.48550/arxiv.1004.2057

openalex publication_date 2010/04/12 · openalex created_date 2019/06/27 · openalex updated_date 2026/07/28

Abstract

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.

Cited by

• Enhanced Sampling Algorithms

Related

• A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation
• Temperature and its control in molecular dynamics simulations
• Benchmarking thermostat algorithms in molecular dynamics simulations of a binary Lennard-Jones glass-former model
• A molecular dynamics method for simulations in the canonical ensemble
• Molecular dynamics simulations at constant pressure and/or temperature