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Title: ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

Abstract

We report that molecular simulation is a scientific tool used in many fields including material science and biology. This requires constant development and enhancement of algorithms within molecular simulation software 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. Furthermore, it has been enhanced by automatic scripts that parse configurations from other established packages, providing scientists with the ability to rapidly set up their simulations.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1]; ORCiD logo [2]; ORCiD logo [3];  [1];  [1]
+ Show Author Affiliations
  1. Max Planck Institute for Polymer Research, Mainz (Germany)
  2. KU Leuven Department of Computer Science, Leuven (Belgium)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1492611
Report Number(s):
LA-UR-18-24195
Journal ID: ISSN 0010-4655
Grant/Contract Number:  
89233218CNA000001; AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Volume: 238; Journal ID: ISSN 0010-4655
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; Multiscale modeling; Coarse graining; Soft matter; Lattice Boltzmann; Molecular simulations; High performance computer; Computational physics

Citation Formats

Guzman, Horacio V., Tretyakov, Nikita, Kobayashi, Hideki, Fogarty, Aoife C., Kreis, Karsten, Krajniak, Jakub, Junghans, Christoph, Kremer, Kurt, and Stuehn, Torsten. ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation. United States: N. p., 2019. Web. doi:10.1016/j.cpc.2018.12.017.
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Guzman, Horacio V., Tretyakov, Nikita, Kobayashi, Hideki, Fogarty, Aoife C., Kreis, Karsten, Krajniak, Jakub, Junghans, Christoph, Kremer, Kurt, & Stuehn, Torsten. ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation. United States. https://doi.org/10.1016/j.cpc.2018.12.017
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Guzman, Horacio V., Tretyakov, Nikita, Kobayashi, Hideki, Fogarty, Aoife C., Kreis, Karsten, Krajniak, Jakub, Junghans, Christoph, Kremer, Kurt, and Stuehn, Torsten. Thu . "ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation". United States. https://doi.org/10.1016/j.cpc.2018.12.017. https://www.osti.gov/servlets/purl/1492611.
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@article{osti_1492611,
title = {ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation},
author = {Guzman, Horacio V. and Tretyakov, Nikita and Kobayashi, Hideki and Fogarty, Aoife C. and Kreis, Karsten and Krajniak, Jakub and Junghans, Christoph and Kremer, Kurt and Stuehn, Torsten},
abstractNote = {We report that molecular simulation is a scientific tool used in many fields including material science and biology. This requires constant development and enhancement of algorithms within molecular simulation software 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. Furthermore, it has been enhanced by automatic scripts that parse configurations from other established packages, providing scientists with the ability to rapidly set up their simulations.},
doi = {10.1016/j.cpc.2018.12.017},
journal = {Computer Physics Communications},
number = ,
volume = 238,
place = {United States},
year = {Thu Jan 03 00:00:00 EST 2019},
month = {Thu Jan 03 00:00:00 EST 2019}
}
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https://doi.org/10.1016/j.cpc.2018.12.017
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