openeuler/namd repository overview

⁠Quick reference

• The official NAMD docker image.

• Maintained by: openEuler CloudNative SIG⁠.

• Where to get help: openEuler CloudNative SIG⁠, openEuler⁠.

⁠NAMD | openEuler

Current NAMD docker images are built on the openEuler⁠. This repository is free to use and exempted from per-user rate limits.

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation and analysis is integrated into the visualization package VMD. Visit the NAMD website for complete information and documentation.

⁠Supported tags and respective Dockerfile links

The tag of each namd docker image is consist of the version of namd and the version of basic image. The details are as follows

⁠Usage

In this usage, users can select the corresponding {Tag} based on their requirements.

• Pull the openeuler/namd image from docker

  docker pull openeuler/namd:{Tag}
  

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• Run with an interactive shell

  You can also start the container with an interactive shell to use NAMD.

  docker run -it --rm openeuler/namd:{Tag} bash
  

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• Single Process Execution

  cd /opt/namd/Linux-ARM64-g++
  /namd3 src/alanin
  

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  This will:

  • Execute the simulation using one CPU core
  • Display progress output in terminal

• Parallel Execution Using Charm++

  cd /opt/namd/Linux-ARM64-g++
  ./charmrun ++local +p2 ./namd3 src/alanin
  

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  This will:

  • Launch 2 parallel proecsses (+p2)
  • Use local communication (++local) on the same machine
  • Distribute computation across avaliable CPU cores

⁠Question and answering

If you have any questions or want to use some special features, please submit an issue or a pull request on openeuler-docker-images⁠.