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MDTools is a collection of generic, ready-to-use scripts to prepare and analyze molecular dynamics (MD) simulations, inspired by and the Gromacs command-line tools.
The main feature of this package is therefore not the package itself, but the Python scripts-label shipped along with this package in the scripts/ directory. These Python scripts are fully functional and directly executable (provided you have installed ) 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 . 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 , you are not limited to Gromacs trajectories but you can read and analyze a variety of different . You also benefit from MDAnalysis' rich .
For you there is no need to interact with the MDTools package directly. You can simply run the scripts and do not need to care about what is happening in the background (although of course you can). Simply install the package, run the scripts and be happy ;). You only need to interact with the MDTools package directly, when
- You want to make changes to the scripts;
- You write your own scripts and want to use functions, classes or other objects defined in the MDTools package;
- You want to
contribute <dev-guide-label>to this package.
MDTools is written in pure Python and is mainly based on the Python packages , , and .
Note
This project is at the beginning. At the moment it is mainly intended for my personal use and will evolve according to my personal needs. However, everybody is welcome to use it and to contribute to it and to write scripts for his/her own purposes. As mentioned above, the aim of this project is to build up a collection of generic Python scripts to prepare and analyze MD simulations. If you want to contribute, please read the .
Warning
The scripts and functions are not (extensively) tested! The only test cases we have so far are the examples from the Examples sections of the docstrings, which are verified using doctest. The plan is to implement extensive unit tests using , but so far we did not had the time for this. Implementing (unit) tests would thus be a great way for you to contribute to this project and it would be highly appreciated.
doc_pages/general_docs/installation doc_pages/general_docs/usage doc_pages/mdtools/mdtools doc_pages/scripts/scripts doc_pages/dev_guide/dev_guide doc_pages/general_docs/references
There exist packages/projects that pursue very similar goals as MDTools. Some of them have a way bigger user community, more contributors and are more actively maintained and developed than MDTools. Therefore, you might consider using these packages instead of or in addition to MDTools. Here is a list of the most notable of these packages:
This list is not comprehensive and only includes packages that we are aware of. Also have a look at the projects that are based on MDAnalysis.
Installation instructions are given in the installation-label section. The basic usage of the scripts is described in the usage-label section.
If you have any questions, feel free to use our forum on . If you encounter a bug or want to request a new feature, please open a new .
If you want to contribute to the project, please read the .
Source code is available from https://github.com/andthum/mdtools under the , version 3. You can download or clone the repository with :
git clone https://github.com/andthum/mdtools.gitMDTools is free software: you can redistribute it and/or modify it under the terms of the 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 for more details.
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