Packmol
Computing Applications (HPC) MIT (Free)
About
A molecular packing tool that creates initial configurations for molecular dynamics simulations by positioning molecules into defined geometric regions (boxes, spheres, cylinders) while avoiding atomic overlaps and steric clashes.
Key Features
- Geometry: boxes, spheres, cylinders, planes
- Constraints: distance, inside/outside regions
- Output: PDB, XYZ coordinate files
- Integration: GROMACS, NAMD, AMBER workflows
Citation
Martinez, L. et al. PACKMOL: A package for building initial configurations for molecular dynamics simulations. J. Comput. Chem. 30, 2157-2164 (2009). DOI:10.1002/jcc.21224
Frequently Asked Questions
What is Packmol?
Packmol is a computing applications (hpc) application available in the Paramus App Store. A molecular packing tool that creates initial configurations for molecular dynamics simulations by positioning molecules into defined geometric regions (boxes, spheres, cylinders) while avoiding atomic overlaps and steric clashes.
Is Packmol free to use?
Yes. Packmol is distributed under the MIT (Free) license and is available at no cost through the Paramus App Store.
How do I install Packmol?
Packmol 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 Packmol for one-click deployment.
What are the key features of Packmol?
Key features of Packmol include: Geometry: boxes, spheres, cylinders, planes; Constraints: distance, inside/outside regions; Output: PDB, XYZ coordinate files; Integration: GROMACS, NAMD, AMBER workflows.
What type of application is Packmol?
Packmol 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 Packmol run on?
Packmol 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 Packmol be automated or integrated with AI workflows?
Yes. Packmol 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 Packmol in publications?
The recommended citation for Packmol is: Martinez, L. et al. PACKMOL: A package for building initial configurations for molecular dynamics simulations. J. Comput. Chem. 30, 2157-2164 (2009). DOI:10.1002/jcc.21224