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Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL

2013; American Chemical Society; Volume: 53; Issue: 5 Linguagem: Inglês

10.1021/ci400071x

1549-960X

Tomasz Makarewicz, Rajmund Kaźmierkiewicz,

RNA and protein synthesis mechanisms

The molecular models stored as PDB formatted files are static, but most of the biomolecular systems display a dynamic behavior, in other words their conformations depend on time. To get the dynamic model from the static one, one needs to perform the molecular dynamics (MD) simulation using tools like GROMACS. This paper describes functionality of the newly created plugin for PyMOL (the popular and easy to use program for displaying and manipulating molecule models). This plugin enables the easy use of molecular dynamics simulations using GROMACS through a graphic interface. It transfers the results of those calculations and displays them back in PyMOL. All the components of the stack are open source and are available free of charge. This strategy gives researchers easy access to the molecular dynamics PYMOL plugin and creates an opportunity to modify its source when needed.