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D4.4: Meso- and multi-scale modelling E-CAM modules III

Authors: Chiacchiera, Silvia; Jony Castagna; Krekeler, Christian;

D4.4: Meso- and multi-scale modelling E-CAM modules III

Abstract

In this report for Deliverable 4.4 of E-CAM, nine software modules in meso– and multi–scale modelling are presented. Four of the modules have been implemented in DL_MESO_DPD: • Ewald method for the GPU version of DL_MESO_DPD • Smooth Particle Mesh Ewald (SPME) method for the GPU version of DL_MESO_DPD • Analysis of local tetrahedral ordering for DL_MESO_DPD • Consistency check of input files in DL_MESO_DPD Five of the modules concern the Grand Canonical Adaptive Resolution Scheme (GC-AdResS) and have been developed, implemented and tested in/with GROMACS 5.1.0 and GROMACS 5.1.5. The patches provided are for GROMACS 5.1.5. The modules provide a recipe to simplify the implementation and to allow to look into a microcanonical (i.e., NVE-like) environment. They are based on the same principles as the Abrupt AdResS modules reported in a previous deliverable D4.3[1]. Furthermore, we provide all the tools necessary to run and check the AdResS simulations. The modules are: • Local Thermostat Abrupt AdResS • Thermodynamic Force Calculator for Abrupt AdResS • Energy (AT)/Energy(interface) ratio: Necessary condition for AdResS simulations • Velocity-Velocity autocorrelation function for AdResS • AdResS-Radial Distribution Function (RDF). A short description is written for each module, followed by a link to the respective Merge-Request on the GitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules. [1] B. Duenweg, J. Castagna, S. Chiacchiera, H. Kobayashi, and C. Krekeler, “Meso– and multi–scale modelling E-CAM modules II,” Mar. 2018. [Online]. Available: https://doi.org/10.5281/zenodo.1210075

Keywords

coarse--graining, DL_MESO_DPD, GC-AdResS, GPU, GROMACS, DPD, electrostatics

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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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