ESPResSo++ 2.0: advanced methods for multiscale molecular simulation

DOI10.1016/J.CPC.2018.12.017MaRDI QIDQ6042327zbMATH OpenOpenAlexWikidataFDO

Authors Horacio V. Guzman, Nikita Tretyakov, Hideki Kobayashi, Aoife C. Fogarty, Karsten Kreis, Jakub Krajniak, Christoph Junghans, Kurt Kremer, Torsten Stuehn

Publication date 10 May 2023

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1806.10841

zbMATH Keywords

coarse grainingcomputational physicshigh performance computerlattice Boltzmannmolecular dynamicsmolecular simulationsmultiscale modelingsoft matter

Mathematics Subject Classification ID

Fluid mechanics (76-XX) Statistical mechanics, structure of matter (82-XX)

Abstract: Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the latest applications of the adaptive resolution scheme, the hydrodynamic interactions through a lattice Boltzmann solvent coupled to particle-based molecular dynamics, the implementation of the hierarchical strategy for equilibrating long-chained polymer melts and a heterogeneous spatial domain decomposition. The software design of ESPResSo++ has kept its highly modular C++ kernel with a Python user interface. Moreover, it was enhanced by automatic scripts parsing configurations from other established packages providing scientists with a rapid setup possibility for their simulations.

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Cited in

(2)

• ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
• Eucb: a C++ program for molecular dynamics trajectory analysis

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