ニュース

2018年08月08日 掲載 (Published 08/08/2018)


「Biophysics and Physicobiology」にRyosuke Iwai et al. “Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replicaexchange frequency, and thermostat coupling time constant”を掲載

日本生物物理学会欧文誌[Biophysics and Physicobiology]に以下の論文が新規掲載されました。

Ryosuke Iwai, Kota Kasahara and Takuya Takahashi a “Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replicaexchange frequency, and thermostat coupling time constant”

【Significance】
Revisiting assessments for influence of adjustable parameters in the replica-exchange molecular dynamics method.

The replica-exchange molecular dynamics (REMD) method is a powerful approach to investigate conformational ensembles of molecular systems. Although this method requires some adjustable parameters, there is no golden standard for setting of the parameters. Effects of the parameters on sampling efficiency and resultant ensemble have been argued. Our evaluation found that shorter intervals for replica-exchange attempts enhance conformational sampling but cause the artifacts due to insufficiency of thermal relaxation. In particular, the ensemble average of temperature deviates from the target temperature of the thermostat. The results of this evaluation will be helpful to adjust the parameters for REMD simulations.


Biophysics and Physicobiology, Vol.15, pp. 165-172

URL:https://www.jstage.jst.go.jp/article/biophysico/15/0/15_165/_article