ESPResSO 3.1: molecular dynamics software for coarse-grained models. (English) Zbl 1269.82007
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 1-23 (2013).
Summary: ESPResSo is a package for molecular dynamics (MD) simulations of coarse-grained models. We present the most recent version (3.1) of our software, highlighting some recent algorithmic extensions to version 1.0 presented in a previous paper [H. J. Limbach et al., “ESPResSo – an extensible simulation package for research on soft matter systems”, Comput. Phys. Commun. 174, No. 9, 704–727 (2006; doi:10.1016/j.cpc.2005.10.005)]. A major strength of our package is the multitude of implemented methods for calculating Coulomb and dipolar interactions in periodic and partially periodic geometries.
Here, we present some more recent additions which include methods for systems with dielectric contrasts that frequently occur in coarse-grained models of charged systems with implicit water models, and an alternative, completely local electrostatic solver that is based on the electrodynamic equations. We also describe our approach to rigid body dynamics that uses MD particles with fixed relative positions. ESPResSo now gained the ability to add bonds during the integration, which allows to study, e.g., agglomeration. For hydrodynamic interactions, a thermalised lattice Boltzmann solver has been built into ESPResSo, which can be coupled to the MD particles. This computationally expensive algorithm can be greatly accelerated by using graphics processing units. For the analysis of time series spanning many orders of magnitude in time scales, we implemented a hierarchical generic correlation algorithm for user-configurable observables.
For the entire collection see [Zbl 1257.65003].
Here, we present some more recent additions which include methods for systems with dielectric contrasts that frequently occur in coarse-grained models of charged systems with implicit water models, and an alternative, completely local electrostatic solver that is based on the electrodynamic equations. We also describe our approach to rigid body dynamics that uses MD particles with fixed relative positions. ESPResSo now gained the ability to add bonds during the integration, which allows to study, e.g., agglomeration. For hydrodynamic interactions, a thermalised lattice Boltzmann solver has been built into ESPResSo, which can be coupled to the MD particles. This computationally expensive algorithm can be greatly accelerated by using graphics processing units. For the analysis of time series spanning many orders of magnitude in time scales, we implemented a hierarchical generic correlation algorithm for user-configurable observables.
For the entire collection see [Zbl 1257.65003].
MSC:
| 82-04 | Software, source code, etc. for problems pertaining to statistical mechanics |
| 76M28 | Particle methods and lattice-gas methods |
| 82-08 | Computational methods (statistical mechanics) (MSC2010) |
| 65Y10 | Numerical algorithms for specific classes of architectures |
| 82D60 | Statistical mechanics of polymers |
Keywords:
molecular dynamics; coarse-graining; Lattice-Boltzmann; extensible simulation package for research on soft matter systemsReferences:
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