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arXiv · 1804.06205

A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions

Hideo Doi·Koji Okuwaki·Takamitsu Naito·Sona Saitou·Yuji Mochizuki
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Abstract

We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a sizable speed-up per step and also a near linear scaling of costs with respect to the number of particles. The other is an easy inclusion of additional specific (such as 1-3 and 1-5 Morse bonding) interactions which are crucial in describing protein structures. The formations of alpha-helix and beta-sheet through DPD were then demonstrated. CAMUS is freely available at the GitHub site.

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Hideo Doi, Koji Okuwaki, Takamitsu Naito, Sona Saitou, Yuji Mochizuki. 2018-04-17. A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions. https://doi.org/10.1273/cbij.18.70

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