NAMD (Nanoscale Molecular Dynamics): Install, Run and Cite

Who this is for: researchers and students who need to find, run and cite NAMD (Nanoscale Molecular Dynamics), the molecular dynamics program from the University of Illinois. After reading you should know whether the licence covers your use, which keywords a minimal run needs, and which files it writes.

Not the same “NAMD”: this page covers the simulation software. The National Association of Medicaid Directors (also abbreviated NAMD) is a health-policy association and is unrelated. “nAMD” with a lowercase n is the common abbreviation for neovascular age-related macular degeneration, an eye condition; see the FAQ below. Nothing here is medical advice.

What NAMD is used for in research

NAMD is a “parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems,” according to the Theoretical and Computational Biophysics Group’s NAMD overview page (read 2026-11-07). It is based on Charm++ parallel objects, scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest, and is file-compatible with AMBER, CHARMM and X-PLOR. The same page says it uses the molecular graphics program VMD for simulation setup and trajectory analysis; see our guide to Visual Molecular Dynamics (VMD) for that side of the workflow.

Recent releases add GPU-offload and GPU-resident modes. The version announced on the NAMD site in July 2026 is NAMD 3.0.3, which fixes a spinAngle wrapping bug in Colvars present in 3.0 to 3.0.2; the site urges users of those versions to upgrade.

Is NAMD free, and what does the licence require?

NAMD is distributed free of charge with source code, but the NAMD licence (read 2026-11-07) limits free use to academic, research and internal business purposes. Commercial use requires a commercial licence; this page does not quote prices.

• Derivative works must be marked as such and renamed.
• Published work that used NAMD must cite Phillips et al., J. Chem. Phys. 153:044130 (2020), doi:10.1063/5.0014475.
• Electronic documents that mention NAMD should link to the official NAMD page.

Recording the exact NAMD version in your methods supports reproducibility; see FAIR4RS and software citation principles and computational environment.

Install or access (official source only)

Get NAMD from the official NAMD page. It offers binaries for many platforms, a source distribution you can build yourself, and Git access to the source. Use the current release listed there (NAMD 3.0.3 at the time of reading).

• Windows: the user’s guide states there are no native Windows builds; on Windows 10 or 11 run the Linux-x86_64-multicore build under WSL2.
• Clusters: the user’s guide describes charmrun with a nodelist file for running across nodes.
• GPU (CUDA and other): NAMD 3 has GPU-offload and GPU-resident modes, and the 2.15 alpha line adds Intel GPU Max support through oneAPI SYCL. Settings are version specific, so follow the GPU Acceleration section of the NAMD 3.0 User’s Guide.

Step-by-step: set up and run a simulation

NAMD is driven by a plain-text configuration file; keywords are case-insensitive. Commands follow the running NAMD section of the user’s guide (read 2026-11-07).

1. Prepare the system files. A run needs initial coordinates, a structure file and force-field parameter files. VMD is the tool NAMD’s site names for simulation setup.
2. Write the configuration file. The configuration file section lists the required parameters: numsteps, coordinates, structure, parameters, exclude, outputname, and one of temperature, velocities or binvelocities. The guide recommends pairlistdist of at least the cutoff plus 1.
3. Test with zero steps. run 0 computes energies only, a quick check that your files and parameters load.
4. Run it.
   • Single core: namd3 myconfig.namd
   • Multicore on one machine: namd3 +p8 myconfig.namd (8 is the number of processors to use)
   • Other multiprocessor builds: charmrun namd3 ++local +p8 myconfig.namd; the full path to namd3 may be needed
5. Request production steps. Replace run 0 with run <steps> once the test passes.

myconfig.namd is a placeholder for your own configuration file name.

Output and how to read it

Per the configuration-file documentation, the outputname basename sets the names of the final-state files:

File	Controlled by	Role
.coor	output / outputname	Output coordinates
.vel	output / outputname	Output velocities
.xsc	output / outputname	Extended system (cell) information
.force	output withforces (adds) or output onlyforces (only)	Forces
DCD file	DCDfile	Trajectory
Restart files	restartname	Restarting a run

Because NAMD’s site names VMD for trajectory analysis, load your structure file and the DCD trajectory there to inspect motion.

Troubleshooting

• Run will not start: check that every required keyword in step 2 is present and that file paths are correct; confirm with run 0 first.
• Launch with charmrun fails to find the program: the user’s guide notes the full path to namd3 may be needed.
• Windows: use WSL2 with the Linux multicore build; there is no native Windows binary.
• Colvars results from 3.0 to 3.0.2: the NAMD site reports a spinAngle wrapping bug fixed in 3.0.3.
• GPU runs: settings depend on the version; follow the GPU Acceleration section of the user’s guide for your release.

Free alternatives

Other molecular dynamics packages with an open-source statement on their own sites (both read 2026-11-07):

Software	How its own site describes it	Licence statement on its site
GROMACS	Software suite for high-performance molecular dynamics and output analysis	Described as free and open-source
LAMMPS	Classical molecular dynamics code focused on materials modelling; runs on one processor or in parallel	Open source under GPLv2

For another open-source simulation tool in a different domain, see our Cantera guide.

FAQ

Is NAMD free to use?

Yes for academic, research and internal business purposes under the NAMD licence; commercial use requires a commercial licence. Source code comes with the free distribution.

What does NAMD mean?

In molecular simulation, NAMD stands for Nanoscale Molecular Dynamics, a program for simulating large biomolecular systems, distributed from the University of Illinois site.

What is NAMD Medicaid?

That is a different organisation: the National Association of Medicaid Directors, which represents state Medicaid agencies. It has no connection to the simulation software.

What does nAMD mean, and what is nAMD in ophthalmology?

In eye care, nAMD is the usual abbreviation for neovascular (wet) age-related macular degeneration. This is a medical topic outside this site’s scope; for questions about eye symptoms or treatment, speak to an ophthalmologist or optometrist. This is general information, not medical advice.

Where are the NAMD download, tutorial and benchmark pages?

Downloads, the license page and the user’s guide are all linked from the official NAMD page. Performance depends on system size and hardware, so benchmark your own system on your own machine.

Sources (official documentation, read 2026-11-07)

• NAMD overview and downloads
• NAMD licence
• NAMD 3.0 User’s Guide: configuration file
• NAMD 3.0 User’s Guide: running NAMD
• GROMACS and LAMMPS home pages
• Phillips JC et al., J. Chem. Phys. 153:044130 (2020), doi:10.1063/5.0014475