MDANSE is a python application designed for computing neutron observables from molecular dynamics (MD) trajectories that 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. Once the beta version has been created, it will be possible to install MDANSE directly from PyPI using pip install.
The untested version of MDANSE can be downloaded from GitHub Actions as a Python wheel. There is one wheel for the main code ('MDANSE'), platform depenedent, and another for the GUI ('MDANSE_GUI'). Once downloaded, they can be installed by typing pip install MDANSE-*.whl. The GUI script can be run using the mdanse_gui command (mdanse_gui.exe on windows).
The typical workflow will look as follows:
- Convert a trajectory from the file format generated by an MD simulation software into a NetCDF format (File>Trajectory conveters)
- Load the converted trajectory into MDANSE (File>Load data)
- Perform an analysis of choice (through the Plugins panel)
- 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 proprietary file formats into MMTK-style NetCDF 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
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, if the trajectory is as expected, various properties can be calculated, which can be compared with neutron (or, some, with X-ray) experimental data, or used as new data to draw conclusions from. The following properties can be computed:
Dynamics
- Angular correlation
- Density of states
- Mean Square Displacement
- Order parameter
- Position Autocorrelation Function
- Velocity Autocorrelation Function
Infrared
- Dipole Autocorrelation Function
Scattering
- Current correlation function
- 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
- Spatial Density
- Static Structure Factor
- Voronoi
- X-Ray Static Structure Factor
Thermodynamics
- Density
- Temperature
Each of these analyses can be configured in various ways. For example, the frames that are used can be changed, certain atoms can be specified to be the only ones for which the property is computed, or specified atoms can be substituted with different elements/isotopes. Finally, their results can be outputted in a NetCDF file, an HDF5 file, or a set of DAT files, 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 and ScientificPython, in order to reduce dependencies and thus facilitate installation.
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 and Remi Perenon.
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
