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MDTools is a collection of generic, ready-to-use Python scripts to prepare and analyze molecular dynamics (MD) simulations, inspired by MDAnalysis and the Gromacs command-line tools.
The main feature of this package is therefore not the package itself, but the Python scripts shipped along with this package in the scripts/ directory. These Python scripts are fully functional and directly executable (provided you have installed Python) without the need to go into the source code.
The idea is to provide the user with a collection of scripts to prepare and analyze MD simulations similar to the command-line tools shipped along with Gromacs. For instance, the script scripts/dynamics/msd_serial.py can be used to calculate the mean square displacement of a given selection (i.e. a user-defined group of atoms). Because MDTools is based on MDAnalysis, you are not limited to Gromacs trajectories but you can read and analyze a variety of different trajectory and topology formats. You also benefit from MDAnalysis' rich selection syntax.
The complete documentation of MDTools including installation and usage instructions can be found here.
If you have any questions, feel free to use the Question&Answer forum on GitHub. If you encounter a bug or want to request a new feature, please open a new Issue.
MDTools is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
MDTools is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.