Article Dans Une Revue Journal of the Physical Society of Japan Année : 2020

A Robust, Symmetric Operator-Composition Integrator for the Berendsen Temperature-Control Molecular Dynamics Equation

Ikuo Fukuda
  • Fonction : Auteur
Haruki Nakamura
  • Fonction : Auteur

Résumé

The Berendsen equations of motion (EOM) are widely used for controlling the temperature of a target physical system in molecular dynamics simulations. Its numerical integration, however, has never raised much attention. Yet, a non-optimal integration scheme de…nitely lowers the e¢ ciency of the EOM. If the integration becomes more robust, then does the Berendsen method. To realize this, we propose an operator composition scheme having the following properties: symmetricity, i.e., time reversibility in the original di¤erential equation is kept; systematic, i.e., any higher order of the local accuracy can be attained; robustness, i.e., a new velocity scaling factor is bounded, which enables faster temperature control. Our extended EOM formalism, which provides an invariant function, also helps to observe the numerical error that cannot be detected solely by the temperature controllability. These properties of the proposed method were con…rmed by applying it into three molecular systems.

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hal-02988433 , version 1 (04-11-2020)

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Séverine Queyroy, Ikuo Fukuda, Haruki Nakamura. A Robust, Symmetric Operator-Composition Integrator for the Berendsen Temperature-Control Molecular Dynamics Equation. Journal of the Physical Society of Japan, 2020, 89 (6), pp.064004. ⟨10.7566/JPSJ.89.064004⟩. ⟨hal-02988433⟩
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