MDANSE is a Python application designed for computing neutron observables from molecular dynamics (MD) trajectories. The results can be directly compared with neutron scattering experiments, particularly inelastic and quasi-elastic neutron scattering spectroscopies.

To do this, it interfaces with a variety of MD simulation software such as CASTEP, VASP, DMOL, Gromacs, DL_POLY, CHARMM, LAMMPS, PBD, DFTB etc., and provides both a graphical user interface (GUI) and a command line interface.

This project is built on the development published previously:
G. Goret, B. Aoun, E. Pellegrini, "MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations", J Chem Inf Model. 57(1):1-5 (2017).

This is the development version of MDANSE. The main difference compared to the previous version is the transition from Python 2 to Python 3, and from wxWidgets to Qt. The previous version, formerly in the 'develop' branch, can now be found in the legacy branch.

The current version of MDANSE is currently still at the alpha stage. You can help it advance to the beta stage by reporting problems you experience while using MDANSE.

We recommend that you install MDANSE in a Python virtual environment. You can create a virtual environment named mdanse_env by typing

python3 -m venv mdanse_env

To activate your virtual environment, type

source mdanse_env/bin/activate

in a bash console, or

mdanse_end\Scripts\activate.bat

if you are using cmd.exe on Windows.

While your virtual environment is active, you can install MDANSE:

pip install MDANSE MDANSE_GUI

and start the graphical interface by typing

mdanse_gui

At the moment MDANSE and MDANSE_GUI are undergoing frequent changes. If you would like to try out the latest development version, you can install directly from GitHub using pip:

python3 -m pip install "git+https://github.com/ISISNeutronMuon/MDANSE@protos#egg=MDANSE&subdirectory=MDANSE"
python3 -m pip install "git+https://github.com/ISISNeutronMuon/MDANSE@protos#egg=MDANSE_GUI&subdirectory=MDANSE_GUI"

The typical workflow of MDANSE:

1. Convert a trajectory from the file format generated by an MD simulation software into the MDANSE trajectory format,
2. Load the converted trajectory into MDANSE,
3. Perform an analysis,
4. Check the results with the plotter.

The most complete user documentation of MDANSE can be found on our Read the Docs page. At the same time, it is still possible to access the original MDANSE User Guide.

Other information including example scripts can be found on the MDANSE website

Firstly, MDANSE can interface with MD simulation software. It does this by providing converters for different file formats into an .MDT file (HDF format), which is then used for all calculations. The following MD packages are supported:

• CASTEP
• CHARMM
• DFTB
• Discover
• DL_POLY
• DMol
• Forcite
• Gromacs
• LAMMPS
• NAMD
• PDB
• VASP
• XPLOR
• ASE

The converted trajectory can then be loaded into MDANSE, where it can be visualised via the Molecular Viewer and animated. Various trajectory variables (positions, velocities, and forces) can also be plotted for each particle. Then, various properties can be calculated, which can be compared with neutron (or, for some analysis types, with X-ray) experimental data, or used as a prediction of results of a potential experiment. The following properties can be computed:

Each of these analyses can be controlled using a number of parameters. For example, the user can select a subset of trajectory frames or a subset of atoms on which to perform the calculation, or specified atoms can be substituted with different elements/isotopes. Finally, their results can be saved in an MDA file (HDF5 format), or a set of DAT files (text format), and those can then be plotted directly in MDANSE.

More detailed information on how MDANSE works, what it can do, and the science can all be found on our Read the Docs page.

If you used MDANSE in your research, please cite the following paper:

MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations. G. Goret, B. Aoun, E. Pellegrini. J Chem Inf Model. (2017) 57(1):1-5.

MDANSE is licensed under GPL-3.0. See LICENSE for more information.

MDANSE started as a fork of version 3 of the nMOLDYN program. nMOLDYN was originally developed by Gerald Kneller in 1995 and subsequently also by Konrad Hinsen, Tomasz Rog, Krzysztof Murzyn, Slawomir Stachura, and Eric Pellegrini. MDANSE includes most of the code of nMOLDYN3, and also code from the libraries MMTK, ScientificPython and MDTraj.

For more information see:

nMoldyn 3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations. K. Hinsen, E. Pellegrini, S. Stachura, G.R. Kneller J. Comput. Chem. (2012) 33:2043-2048 [https://doi.org/10.1002/jcc.23035][https://doi.org/10.1002/jcc.23035].

We are grateful to all the people who have helped in some way or another to improve nMOLDYN and/or MDANSE along those years. Apart from the main developers mentioned above, we would like to acknowledge explicitly the contributions done in the past by Bachir Aoun, Vania Calandrini, Paolo Calligari, Gael Goret, Remi Perenon and Rastislav Turanyi.

The MDANSE project is supported by Ada Lovelace Centre, ISIS Neutron and Muon Source, Science and Technology Facilities Council, UKRI, and the Institut Laue-Langevin (Grenoble, France). Past financial support from the French Agence Nationale de la Recherche (ANR) through contracts No. ANR-2010-COSI-001-01 and ANR-06-CIS6-012-01, and the Horizon 2020 Framework Programme of the European Union under project number 654000 is also acknowledged.

MDANSE is currently maintained and developed by software developers from ISIS and ILL, but we are fully open to new collaborators who would like to contribute code, documentation, tutorials or usage examples. If you want to join the project contact:

Dr. Sanghamitra Mukhopadhyay ([email protected])
ISIS Neutron and Muon Source
Rutherford Appleton Laboratory
Didcot, UK

For questions or contributions related to the software, please contact:

Dr. Maciej Bartkowiak ([email protected])
ISIS Neutron and Muon Source
Rutherford Appleton Laboratory
Didcot, UK