期刊
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN
卷 79, 期 7, 页码 -出版社
PHYSICAL SOC JAPAN
DOI: 10.1143/JPSJ.79.074001
关键词
generalized-ensemble algorithm; replica-exchange method; molecular dynamics simulation; Gaussian constraint method; Langevin dynamics; Andersen algorithm; Nose-Hoover thermostat; Nose-Poincare thermostat
资金
- Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)
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 article, we present momentum rescaling formulae for four other commonly used constant-temperature algorithms, namely, Langevin dynamics, Andersen algorithm, Nose-Hoover thermostat, and Nose-Poincare 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.
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