Journal Article

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

Kraka, Elfi, Nanayakkara, Sadisha, Tao, Yunwen, Zou, Wenli

2020

Overview

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q–Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

• Publisher: Springer Berlin Heidelberg,Springer Nature B.V
• Subject: Characterization and Evaluation of Materials / Chemical bonds / Chemistry / Chemistry and Materials Science / Computer Appl. in Life Sciences / Computer Applications in Chemistry / Computer programs / Geometry / Lattice vibration / Mathematical analysis / Molecular Medicine / Open source software / Post-processing / Python / Quantum chemistry / Software / Software Report / Theoretical and Computational Chemistry / User interface / User needs / Vibration / Vibration mode / Vibrations