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.
Highlights
Structures of molecules obtained from X-ray crystallography [1], nuclear magnetic resonance [2], and other methods [3] are stored in the Protein Data Bank [4, 5]
First the GROMACS pdb2gmx [35] or x2top [36] tool will be started to convert the PDB formatted file into the format required by GROMACS, which is suitable for further calculations
The Dynamics PyMOL plugin was enhanced with tons of features including: displaying the results of molecular dynamics (MD) with vectors, options to use implicit solvents, window supporting an interpretation of MD, ability to use x2top as an optional GROMACS tool, easy set up of the desired length of simulation, water box optimization, better GROMACS error and warning handling, support for Mac OS X, removing Tix dependence
Summary
Structures of molecules obtained from X-ray crystallography [1], nuclear magnetic resonance [2], and other methods [3] are stored in the Protein Data Bank [4, 5] They are formatted as PDB files [6] and one of the most popular software to visualize them is PyMOL [7]. The water box, if used without the proper periodic boundary conditions, would lead to undesired border effects, which could disturb the whole simulation Those limitations were stimulus to develop other methods of handling solvent in molecular dynamics simulations. GROMACS offers implicit solvent as an alternative and exposes three generalized Born (GB) implementations: Still, Hawkins-Cramer-Truhlar (HCT), Onufriev-Bashford-Case (OBC) [16] Those implementations offer significant time reduction for molecular dynamics calculations and the reduction of system complexity makes it easier to avoid the risk of simulation failure [17]
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