MDAnalysis
Computing Applications (HPC) GPL-2.0 (Free)
About
Program to analyze trajectories from molecular dynamics simulations. It supports many file formats (CHARMM, DL_POLY, GROMACS, LAMMPS, NAMD, Amber) and allows for distance calculations, RMSD, and complex analysis.
Key Features
- Formats: DCD, XTC, TRR, NetCDF, PDB
- Analysis: RMSD, RMSF, RDF, contacts
- Selection: MDAnalysis atom selection language
- Integration: NumPy, SciPy, parallel
Citation
Michaud-Agrawal, N. et al. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32, 2319-2327 (2011). DOI:10.1002/jcc.21787
Frequently Asked Questions
What is MDAnalysis?
MDAnalysis is a computing applications (hpc) application available in the Paramus App Store. Program to analyze trajectories from molecular dynamics simulations. It supports many file formats (CHARMM, DL_POLY, GROMACS, LAMMPS, NAMD, Amber) and allows for distance calculations, RMSD, and complex analysis.
Is MDAnalysis free to use?
Yes. MDAnalysis is distributed under the GPL-2.0 (Free) license and is available at no cost through the Paramus App Store.
How do I install MDAnalysis?
MDAnalysis is installed through Paramus Chemistry OS, an on-premise Windows platform for computational chemistry. Open the Paramus App Store in your local installation and select MDAnalysis for one-click deployment.
What are the key features of MDAnalysis?
Key features of MDAnalysis include: Formats: DCD, XTC, TRR, NetCDF, PDB; Analysis: RMSD, RMSF, RDF, contacts; Selection: MDAnalysis atom selection language; Integration: NumPy, SciPy, parallel.
What type of application is MDAnalysis?
MDAnalysis belongs to the “Computing Applications (HPC)” category in the Paramus App Store. It runs on Paramus Chemistry OS and can also be accessed through Paramus Cloud for supported workflows.
What platform does MDAnalysis run on?
MDAnalysis runs on Paramus Chemistry OS, a Windows-based on-premise platform that provides local compute power for demanding simulations. It requires a Paramus OS installation with appropriate hardware resources.
Can MDAnalysis be automated or integrated with AI workflows?
Yes. MDAnalysis is available as part of the Paramus ecosystem which supports MCP (Model Context Protocol) tools for AI-driven automation. This enables integration with large language models and automated research pipelines.
How should I cite MDAnalysis in publications?
The recommended citation for MDAnalysis is: Michaud-Agrawal, N. et al. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32, 2319-2327 (2011). DOI:10.1002/jcc.21787