Titel
Pytim: A python package for the interfacial analysis of molecular simulations
Autor*in
Balázs Fábián
Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche‐Comté
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Abstract
Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations. The code implements several algorithms for the identification of instantaneous interfaces of arbitrary shape, and analysis tools written specifically for the study of interfacial properties, such as intrinsic profiles. The code is written in the python language, and makes use of the numpy and scipy packages to deliver high computational performances. Pytim relies on the MDAnalysis library to analyze the trajectory file formats of popular simulation packages such as gromacs, charmm, namd, lammps or Amber, and can be used to steer OpenMM simulations. Pytim can write information about surfaces and surface atomic layers to vtk, cube, and pdb files for easy visualization. The classes of Pytim can be easily customized and extended to include new interfacial algorithms or analysis tools. The code is available as open source and is free of charge.
Stichwort
interfacial analysismolecular simulationspython
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:998485
Erschienen in
Titel
Journal of Computational Chemistry
Band
39
Ausgabe
25
Seitenanfang
2118
Seitenende
2125
Verlag
Wiley
Erscheinungsdatum
2018
Zugänglichkeit
Rechteangabe
© 2018 The Authors

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