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, MDANSE reads trajectories created with 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 2.x branch of MDANSE, which consists of two Python packages, MDANSE (the analysis code) and MDANSE_GUI (the user interface). The final version in the 1.5.x series can still be found in the legacy branch, but is not being actively developed.
The current version of MDANSE is currently still at the beta stage. You can help it advance to the official release 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:
- Convert a trajectory from the file format generated by an MD simulation software into the MDANSE trajectory format,
- Load the converted trajectory into MDANSE,
- Perform an analysis,
- 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 while the most recent tutorials are stored in the MDANSE examples repository.
Firstly, MDANSE can read the output of 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 and animated. Then, various properties can be calculated from the positions and velocities of atoms. The results can be compared with neutron (or, for some analysis types, with X-ray or IR) experimental data, or used as a prediction of results of a potential experiment.
The following properties can be computed:
Dynamics
- Angular correlation
- Density of states
- Mean Square Displacement
- Position Autocorrelation Function
- Velocity Autocorrelation Function
- Current Correlation Function
- van Hove function (self)
- van Hove function (distinct)
Infrared
- Dipole Autocorrelation Function
- Infrared
Scattering
- Dynamic Coherent Structure Factor
- Dynamic Incoherent Structure Factor
- Elastic Incoherent Structure Factor
- Gaussian Dynamic Incoherent Structure Factor
- Neutron Dynamic Total Structure Factor
Structural
- Area Per Molecule
- Coordination Number
- Density Profile
- Eccentricity
- Molecular Trace
- Pair Distribution Function
- Root Mean Square Deviation
- Root Mean Square Fluctuation
- Radius of Gyration
- Solvent Accessible Surface
- Static Structure Factor
- Voronoi (volume per atom)
- X-Ray Static Structure Factor
Thermodynamics
- Density
- Temperature
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) and plotted directly in MDANSE, or saved a set of DAT files (text format) to be processed by the user using their own software of choice.
More detailed information on how MDANSE works, what it can do, and the science can 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 (sanghamitra.mukhopadhyay@stfc.ac.uk)
ISIS Neutron and Muon Source
Rutherford Appleton Laboratory
Didcot, UK
You are welcome to use the issue tracker to submit ideas for extending the MDANSE code or to report problems you encountered. However, if you prefer to contact the MDANSE developers directly, you can send us a message:
MDANSE Help (MDANSE-help@stfc.ac.uk)