Pytim: A python package for the interfacial analysis of molecular simulations

Marcello Sega, György Hantal, Balázs Fábián, P. Jedlovszky

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
JournalJournal of Computational Chemistry
DOIs
Publication statusAccepted/In press - Jan 1 2018

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Keywords

  • interfacial analysis
  • molecular simulations
  • python

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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