NAMD
Nanoscale Molecular Dynamics
Computing Applications (HPC) UIUC-NAMD (Partial)
About
A parallel molecular dynamics engine for simulating large biomolecular systems, supporting CHARMM, AMBER, and OPLS force fields with free energy perturbation, replica exchange, and QM/MM capabilities.
Key Features
- Force fields: CHARMM, AMBER, OPLS
- Methods: FEP, replica exchange, QM/MM
- Scalability: MPI, GPU acceleration
- Integration: VMD visualization
Free for academic use. Commercial license required from UIUC.
Citation
Phillips, J.C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020). DOI:10.1063/5.0014475
Frequently Asked Questions
What is NAMD?
NAMD is a computing applications (hpc) application available in the Paramus App Store. A parallel molecular dynamics engine for simulating large biomolecular systems, supporting CHARMM, AMBER, and OPLS force fields with free energy perturbation, replica exchange, and QM/MM capabilities.
What license does NAMD require?
NAMD is distributed under the UIUC-NAMD (Partial) license. Commercial use may require a separate license. License compliance is verified during Paramus OS registration.
How do I install NAMD?
NAMD 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 NAMD for one-click deployment.
What are the key features of NAMD?
Key features of NAMD include: Force fields: CHARMM, AMBER, OPLS; Methods: FEP, replica exchange, QM/MM; Scalability: MPI, GPU acceleration; Integration: VMD visualization.
What type of application is NAMD?
NAMD 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 NAMD run on?
NAMD 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 NAMD be automated or integrated with AI workflows?
Yes. NAMD 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 NAMD in publications?
The recommended citation for NAMD is: Phillips, J.C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020). DOI:10.1063/5.0014475