Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations

Yoshiharu Mori; Yuko Okamoto

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arXiv · 1206.0348

Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations

Yoshiharu Mori·Yuko Okamoto

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Abstract

A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed in order to study the intramolecular proton transfer reaction of malonaldehyde in aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.

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Yoshiharu Mori, Yuko Okamoto. 2012-06-02. Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations. https://arxiv.org/abs/1206.0348

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