Ensembler: a simple package for fast prototyping and teaching molecular simulations

Benjamin Ries; Stephanie M. Linker; David F. Hahn; Gerhard König; Sereina Riniker

doi:10.1021/acs.jcim.0c01283

Ensembler: a simple package for fast prototyping and teaching molecular simulations

Benjamin Ries
, Stephanie M. Linker
, David F. Hahn
, Gerhard König
, Sereina Riniker^*

^*Corresponding author for this work

Swiss Federal Institute of Technology Zurich

Research output: Contribution to journal › Article › peer-review

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Abstract

Ensembler is a Python package that enables method prototyping using 1D and 2D model systems and allows deepening of the understanding of different molecular dynamics (MD) methods, starting from basic techniques to enhanced sampling and free-energy approaches. The ease of installing and using the package increases shareability, comparability, and reproducibility of scientific code developments. Here, we describe the implementation and usage of the package and provide an application example for free-energy calculation. The code of Ensembler is freely available on GitHub at https://github.com/rinikerlab/Ensembler.

Original language	English
Pages (from-to)	560-564
Number of pages	5
Journal	Journal of Chemical Information and Modeling
Volume	61
Issue number	2
DOIs	https://doi.org/10.1021/acs.jcim.0c01283
Publication status	Published - 29 Jan 2021

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SDG 9 Industry, Innovation, and Infrastructure

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10.1021/acs.jcim.0c01283

Ensembler
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.0c01283.
Accepted author manuscript (Post-print), 459 KB

Cite this

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abstract = "Ensembler is a Python package that enables method prototyping using 1D and 2D model systems and allows deepening of the understanding of different molecular dynamics (MD) methods, starting from basic techniques to enhanced sampling and free-energy approaches. The ease of installing and using the package increases shareability, comparability, and reproducibility of scientific code developments. Here, we describe the implementation and usage of the package and provide an application example for free-energy calculation. The code of Ensembler is freely available on GitHub at https://github.com/rinikerlab/Ensembler.",

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Ensembler: a simple package for fast prototyping and teaching molecular simulations

Abstract

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