MDynaMix
Computing Applications (HPC) GPL-2.0 (Free)
About
General purpose molecular dynamics simulation package for molecular liquids, solutions, and interfaces. Supports NVE, NVT, and NPT ensembles with periodic and slab boundary conditions.
Skills
MCP skills available for MDynaMix, callable from AI workflows and the Paramus chat:
- Analysis — Analyze MD trajectory properties
- Diffusion — Run MDynamix diffusion-coefficient analysis (Layer 3).
- Equilibration — Run standard equilibration protocol
- Info — Get MDynamix service status and capabilities
- Msd — Run MDynamix mean-square displacement analysis (Layer 3).
- Npt — Run NPT (isothermal-isobaric) molecular dynamics
- Nve — Run NVE (microcanonical) molecular dynamics
- Nvt — Run NVT (canonical) molecular dynamics at constant temperature
- Rdf — Run MDynamix radial distribution function analysis (Layer 3).
Browse the full MDynaMix skill documentation
Citation
Lyubartsev, A.P.; Laaksonen, A. MDynaMix – a scalable portable parallel MD simulation package. Computer Physics Communications 128, 565-589 (2000). DOI:10.1016/S0010-4655(99)00529-9
Frequently Asked Questions
What is MDynaMix?
MDynaMix is a computing applications (hpc) application available in the Paramus App Store. General purpose molecular dynamics simulation package for molecular liquids, solutions, and interfaces. Supports NVE, NVT, and NPT ensembles with periodic and slab boundary conditions.
Is MDynaMix free to use?
Yes. MDynaMix is distributed under the GPL-2.0 (Free) license and is available at no cost through the Paramus App Store.
How do I install MDynaMix?
MDynaMix 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 MDynaMix for one-click deployment.
What type of application is MDynaMix?
MDynaMix 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 MDynaMix run on?
MDynaMix 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 MDynaMix be automated or integrated with AI workflows?
Yes. MDynaMix 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 MDynaMix in publications?
The recommended citation for MDynaMix is: Lyubartsev, A.P.; Laaksonen, A. MDynaMix – a scalable portable parallel MD simulation package. Computer Physics Communications 128, 565-589 (2000). DOI:10.1016/S0010-4655(99)00529-9