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NAMD

License information

NAMD can only be installed by users as the download requires accepting the license first. NAMD is covered by a non-exclusive, non-commercial license that can be found on the "NAMD License" page of the NAMD web site.

Note that according to the LUMI Conditions of Use it is the User's responsibility to respect the software license terms. The EasyConfigs provided in the LUMI-EasyBuild-contrib repository do not imply that you have the right to use the software on LUMI.

The NAMD licensse aggreement also explictly requires that the use of NAMD is acknoledged in any publication or report using the citation:

NAMD was developed by the Theoretical Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign.

All published work should also include the following reference:

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Scalable molecular dynamics on CPU and GPU architectures with NAMD. Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475"

Electronic documents will include a direct link to the official NAMD page
at http://www.ks.uiuc.edu/Research/namd/

(The above text copied from the NAMD 2.14 license and may evolve over time!)

User documentation

NAMD requires signing up for a license before you can get access to the sources. Hence EasyBuild cannot download the sources itself and you will have to provide the source tarball to EasyBuild.

To download and install NAMD:

  1. Downloads can be found on the "Software Downloads" page of the NAMD web site.

  2. Look for the version that corresponds with the EasyConfig version and download via the "Source Code" link. This will ask you to log in and offer you the opportunity to register if you haven't done so yet.

    You'll have to do that from your desktop.

  3. On LUMI, create a temporary directory somewhere (e.g., in your home directory) and upload the NAMD sources to that directory.

    Alternatively you can put the sources in the $EBU_USER_PREFIX/sources/n/NAMD subdirectory (assuming you are using that environment variable to point to your EasyBuild installation, otherwise this would be $HOME/EasyBuild/sources/n/NAMD).

  4. You're now ready to start the installation. Make sure that your EasyBuild environment is set up properly and load the suitable LUMI and partition modules and the EasyBuild-user module.

    From within the temporary directory in which you put the source tarball, run the eb command using the flag -r . which tells EasyBuild to also consider the current directory for EasyConfigs and source files. Eg.g, to install NAMD with the NAMD-2.14-cpeGNU-22.08-MPI.eb recipe, execute:

    eb NAMD-2.14-cpeGNU-22.08-MPI.eb -r .

User-installable modules (and EasyConfigs)

Install with the EasyBuild-user module: 

eb <easyconfig> -r
To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider NAMD/<version>.

EasyConfig:

Technical documentation

General information

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

EasyBuild

Version 2.14 for CPE GNU 21.08

  • The EasyConfig is derived from the CSCS one

Version 3.0b6 GPU resident for CPE AMD 23.09

  • Works with a single node runs only - uses multicore Charm++ runtime (no MPI)
  • Beta release of the code
  • Uses ROCm 5.6.1 not fully supported with CPE 23.09

Archived EasyConfigs

The EasyConfigs below are additonal easyconfigs that are not directly available on the system for installation. Users are advised to use the newer ones and these archived ones are unsupported. They are still provided as a source of information should you need this, e.g., to understand the configuration that was used for earlier work on the system.