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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids.

Yunwen Tao¹, Wenli Zou², Sadisha Nanayakkara¹

¹Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA.

Journal of Molecular Modeling

|September 28, 2020

Summary

PyVibMS is a new PyMOL plugin for visualizing molecular and solid system vibrations. This open-source tool supports data from major quantum chemistry programs, offering powerful and user-friendly visualization capabilities.

Keywords:

Harmonic approximation Local vibrational mode theory Normal mode Phonon PyMOL Vibrational spectroscopy

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Area of Science:

Computational Chemistry
Materials Science
Molecular Dynamics

Background:

Visualizing vibrational motions from ab initio calculations requires specialized post-processing tools.
Existing methods may lack compatibility with diverse quantum chemical software packages.

Purpose of the Study:

To develop a versatile PyMOL plugin, PyVibMS, for visualizing vibrational motions.
To enable visualization of both molecular and solid-state vibrational modes.
To support data from widely-used quantum chemistry programs.

Main Methods:

Developed PyVibMS as a plugin for the PyMOL molecular visualization system.
Implemented PyVibMS in Python, ensuring flexibility and sustainability.
Integrated support for vibrational data from Gaussian, Q-Chem, VASP, and CRYSTAL.

Main Results:

PyVibMS successfully visualizes molecular and lattice vibrations.
The plugin offers powerful functionalities and a user-friendly interface.
Demonstrated visualization of Konkoli-Cremer local vibrational modes for the first time.

Conclusions:

PyVibMS provides a valuable, open-source solution for visualizing vibrational analyses.
The plugin enhances the accessibility and utility of computational chemistry results.
PyVibMS is freely available, promoting collaborative research in computational materials science.