Run GROMACS within PyMol with Dynamics


Introduction

GROMACS is a well-known and broadly used suite for molecular dynamics simulations. It is a free, open-source software that supports several force-fields (GROMOS, AMBER, CHARM, etc …) and is one of the flagship software within BioExcel. PyMol is a popular 3D molecular visualization system, maintained and distributed by Schrödinger on an open-source foundation. It provides a solid API that allows flexible customization and the integration of third-party software.

We introduce here a recent plugin, Dynamics, that powers directly GROMACS into PyMol. This plugin is developed by Tomasz Makarewicz and Rajmund Kaźmierkiewicz at the Laboratory of Biomolecular Systems Simulation at the University of Gdańsk. Its main purpose is to perform molecular dynamics simulations using GROMACS directly in a PyMol instance, taking advantage of PyMol’s object representation and selection, and to enable the molecular visualization of MD trajectories in PyMOL loaded molecules. In addition, some visual aids are provided by the plugin for a better understanding of the simulation results.

 

License

This software (including its Debian packaging) is available under the GPL-3 terms. Software is created and maintained by the Laboratory of Biomolecular Systems Simulation at the University of Gdańsk.

Plugin installation

Just like most PyMol plugins, this one can be installed through the standard Plugin section of PyMol. (Note that this section does not exist in the regular version of MacPyMol, you will need to use the X11 Hybrid version as described here).

Requirements

All you need is bash, Python (including Tkinter module), PyMol and GROMACS. If you are not working on a native linux, you also need to download the github repository of the project.

GUI installation

Go to Plugin -> Plugin Manager -> Install New Plugin.
In the section Install from local file, choose the file pymol_plugin_dynamics.py from the downloaded github repository.

Ubuntu installation

In a terminal, type the following commands:

Usage

Once installed, the plugin is accessible from the Plugin section under Dynamics 2.1.0pre. Its main interface (see snapshot below) provides control over many options: the molecule group you want to select (left panel), the force-field and water models you want to use (central panel) and the different parameters of your MD simulation, with the possible addition of positional restraints (right panel). Those restraints are based on atom IDs that are either extracted from the PDB and filtered depending on the atom group chosen on the left panel or directly selected in the PyMol viewer (tip: you need to close and open the Restraints selection window each time you update your PyMol selection in order to update the atom list).

It is possible to start a simulation either by loading a molecule in PyMol from your computer or by restoring a former system from the Previous Projects list. Restoring a former project does not only load the 3D object but also resumes the simulation parameters used by the time. It is also possible to import your own MD parameter files (.mdp files) by copying them to the folder /home/user/.dynamics/ . Watch out, they should be named em.mdp, pr.mdp and md.mdp to respectively match the Energy Minimisation step, the Progression Retrained step and the Molecular Dynamics step! Once set up, you can proceed with your simulation and click on OK. A new window called Calculation Window will pop-up.

From there, you have a very simple interface over your simulation and a progression bar to visualize the progression of your MD simulation. It is possible to save your project before and after it has been executed. It is saved as an archive folder containing all necessary input files (parameters and structures). Once started, the back-end program, GROMACS, will execute the different simulation steps from Calculating topology using Force fields to Creating Multimodel PDB.

One of the nice feature of Dynamics is that it enables the visualization of the simulation trajectory  by automatically loading the generated models into your initial PyMOL molecule. To facilitate the analysis of the MD trajectory, another interface called MD Interpretation takes advantage of PyMol’s representation to provide comprehensive aids to the user. At last, provided you installed ProDy on your system, this plugin can also allow you to visualize the the different normal mode vectors under the form of a PyMol multi-states object.

From our personal experience, the main contributor to this plugin, Tomasz Makarewicz, is very reactive and releases updates on a regular basis. 

If you have any comment, do not hesitate to use the IM-IG forum!

 

 

References

Makarewicz, Tomasz, and Rajmund Kaźmierkiewicz. “Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL.” (2013): 1229-1234.
Makarewicz, Tomasz, and Rajmund Kaźmierkiewicz. “Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis.Journal of molecular modeling 22.5 (2016): 1-7

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