scipion-chem-gromacs

Gromacs is a free and open-source software suite for high-performance Molecular Dynamics (MD) and output analysis. In Scipion-chem-gromacs, we have integrated tools for preparing MD systems, running simulations and modifying and analyzing the output trajectories.

Installation

A) Requirements

In order to use this plugin, you need to install first scipion-chem.

B) Installation steps

Install the stable version

Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager, or

scipion3 installp -p scipion-chem-gromacs

Developer’s version

Download repository:

git clone https://github.com/scipion-chem/scipion-chem-gromacs.git

Install:

scipion3 installp -p /path/to/scipion-chem-gromacs --devel

Warning

Installation of the stable version through the Plugin Manager or with the command provided above is not available yet.

Please install the developer version until a stable version is released, or install the latest stable version with the following steps:

cd /path/to/scipion-chem-gromacs && git checkout master && scipion3 installp -p . --devel

Protocols

Gromacs system preparation: Prepares a Gromacs MD system prior to its simulation from a AtomStruct object.
Gromacs Molecular Dynamics (MD) Simulation: Takes the prepared Gromacs system and use it to run a defined simulation.
Gromacs system modification: Performs modifications over a Gromacs System, specially over its trajectory.