「Biophysics and Physicobiology」に Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi Higo による "myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" を掲載

2020年11月06日 学会誌

日本生物物理学会欧文誌［Biophysics and Physicobiology］に以下の論文が公開されました。

Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi Higo
"myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling"

【Significance】
A major update of the molecular dynamics (MD) simulation engine myPresto/omegagene is presented. The myPresto/omegagene software has several unique features, including an efficient calculation of electrostatic potentials using the zero-multipole summation method and enhanced sampling from our original methods. In this update, two new functionalities were implemented: (i) a virtual-system coupled canonical MD (VcMD) method for enhanced conformational sampling, along with multi-dimensional reaction coordinate space, and (ii) a coarse-grained model to investigate higher-order molecular assembly. The use of these new functionalities is described in the step-by-step tutorial attached to the software. This article briefly introduces these functionalities and an example.

Biophysics Physicobiology, Vol.17, pp140-146


URL: https://doi.org/10.2142/biophysico.BSJ-2020013