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

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 umpy and 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

Hydrogen bond dynamics of interfacial water molecules revealed from two-dimensional vibrational sum-frequency generation spectroscopy

“…Furthermore, ALMO-EDA calculations [30][31][32] were performed for all configurations along the trajectory, which were separated by 10 fs, using the CP2K 43 code. Interfacial water molecules were obtained using the identification of truly interfacial molecules (ITIM) algorithm 44 .…”

An octanol hinge opens the door to water transport

“…Thus, H 2 O that is distributed in the bulk octanol phase will be mistakenly counted as “truly” interfacial H 2 O in the algorithm. To avoid this issue, a density based cluster approach (Pytim DBSCAN 53 ) is adopted to separate the H 2 O molecules that have penetrated the octanol phase vs. the truly interfacial H 2 O molecules that remain connected to the aqueous phase via a hydrogen bond network. Octanol molecules are counted as truly interfacial if their –OH is hydrogen-bonded to at least one truly interfacial H 2 O molecule.…”

“…Pytim, a python package that has implemented cutoff-based clustering and DBSCAN density-based cluster algorithm, was employed for the cluster search to identify hydrogen bonded clusters consisting solely of octanol or octanol and water and their position within the interfacial region during water transport. 53 Octanol or water molecules are considered to be in the same cluster if their O-atoms are closer than 3.5 Å, which is the O...O distance criterion for a HB.…”

Time-dependent vibrational sum-frequency generation spectroscopy of the air-water interface

“…These two-body donor-acceptor interactions ΔE D!A are a consequence of the delocalization of electrons from the occupied orbitals of a donor molecule D to the virtual orbitals of an acceptor molecule A. The identification of interfacial water molecules at the air-water system was done using the algorithm for the identification of truly interfacial molecules (ITIM) 68,69 . The algorithm uses a probe sphere to detect the molecules at the surface.…”