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Updated: Mar 22, 2026
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
Published on: August 9, 2024
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA
Tomasz Makarewicz1, Rajmund Kaźmierkiewicz2
1Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
Abstract:
In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy library, possibility to use the implicit solvents, an ability to interpret the MD simulations, and implementation of some more GROMACS functionality.
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