[Published online Journal of Computer Chemistry, Japan Vol.24, 1-9, by J-STAGE]
<Title:> ゆらぎの定理を利用した自由エネルギー計算に関する理論的背景と非平衡分子動力学シミュレーションへの応用
<Author(s):> 束村 晴, 菅波 祐介, 赤津 裕哉, 髙橋 颯人, 西村 好史, 中井 浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Enhanced sampling methods have been applied to handle chemical reactions rarely observed in limited-scale molecular dynamics simulations. Some of these methods intentionally put the system in a nonequilibrium state. We focus on free energy calculation methods based on the fluctuation theorem to directly estimate free energy from simulations of nonequilibrium systems. In this paper, we derive Jarzynski’s equality and Bennett acceptance ratio method, and present their illustrative applications to free energy calculation.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0033/_article/-char/ja/
<Title:> ゆらぎの定理を利用した自由エネルギー計算に関する理論的背景と非平衡分子動力学シミュレーションへの応用
<Author(s):> 束村 晴, 菅波 祐介, 赤津 裕哉, 髙橋 颯人, 西村 好史, 中井 浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Enhanced sampling methods have been applied to handle chemical reactions rarely observed in limited-scale molecular dynamics simulations. Some of these methods intentionally put the system in a nonequilibrium state. We focus on free energy calculation methods based on the fluctuation theorem to directly estimate free energy from simulations of nonequilibrium systems. In this paper, we derive Jarzynski’s equality and Bennett acceptance ratio method, and present their illustrative applications to free energy calculation.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0033/_article/-char/ja/
