qtools is a toolset comprised of a Python library Qpyl and a set of command-line tools, for use with the molecular dynamics simulation package Q. This open-source project was created by Miha Purg (currently at Uppsala University) in order to provide Q-users with a set of well-tested tools for automating repetitive and/or tedious tasks, debugging simulations, and analysing results. The author strives to achieve a good balance between the level of user-control over Q (i.e., relatively low abstraction level) and the ease-of-use provided by qtools.
Disclaimer: qtools is not affiliated with Q nor should it be considered an official toolset for Q.
- Python API for interfacing with Q executables.
- EVB mapping and automatic fitting of off-diagonal and gas shift parameters.
- Support for quantum classical path and group exclusion calculations.
- Linear response approximation (LRA) calculations (including group contributions)
- Parameter conversions (OPLS, Amber/GAFF).
- FEP file generation for EVB simulations.
- Input generation for MD/FEP simulations and EVB calculations.
- Output parsing and analysis of MD, FEP and EVB.
- Graphical tool for visualizing results and debugging simulations:
- Free energy profiles
- LRA, REORG, group contributions
- Energy breakdown (VDW, El, Bonds, ...)
The library and tools do not have any dependencies, except matplotlib which is required only for q_plot.py, a non-essential utility used mostly for troubleshooting simulations.
The only requirement is Python, version 2.7
Note: The command-line tools were designed to work in a typical high-perfomance-computer Unix environment, and have not been tested with Microsoft Windows.
Clone the repository to your local directory:
mkdir -p ~/bin && cd ~/bin
git clone https://github.com/mpurg/qtools
Add this line to your ~/.bashrc or ~/.bash_profile:
source $HOME/bin/qtools/qtools_init.sh
Run the CLI config script:
qscripts_config.py
The starting point should be the docs/tutorials folder.
It contains working examples of how you can use the command line tools to prepare, simulate and analyse a simple SN2 reaction with EVB. Additionally, a recently published chapter in the serial Methods in Enzymology provides step-by-step instructions for performing EVB simulations on a real enzymatic system with qtools. Manuscript available here (paywalled).
For those inclined on using the Python API directly, jupyter-notebook examples calling the Qpyl API can be found in docs/examples. The API reference can be found in docs/api/html. Additionally, the tests, and the command-line interface (qscripts-cli) can be useful to explore the API.
Automated Testing is performed on Travis-CI,
with pytest for Qpyl
(code coverage).
and simple regression tests for CLI tools.
To run the tests locally, make sure you have pytest installed and simply type:
cd tests
./run_tests.sh
To acknowledge the use of qtools in scientific publications, please specify the version and the
DOI of the latest release:
Example:
...analysis was performed with qtools v0.5.10 (DOI: 10.5281/zenodo.842003).
Miha Purg (miha.purg@gmail.com)
Paul Bauer