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Pytim: A python package for the interfacial analysis of molecular simulations
Author(s) -
Sega Marcello,
Hantal György,
Fábián Balázs,
Jedlovszky Pál
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25384
Subject(s) - python (programming language) , computer science , computational science , visualization , programming language , computer graphics (images) , source code , data mining
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 n umpy and s cipy 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. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc