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

TL;DR

This paper introduces CAMUS, a portable Fortran code for DPD simulations that speeds up calculations by avoiding neighbor lists and easily incorporates specific interactions, enabling protein structure modeling.

Contribution

The code uniquely combines speed and flexibility, allowing efficient DPD simulations with specific interactions for biological structures.

Findings

Demonstrated formation of alpha-helix and beta-sheet structures

Achieved near linear scaling with particle number

Enabled easy inclusion of specific interactions

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.