NAMD
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
General
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.
- Project web site: http://www.ks.uiuc.edu/Research/namd/
- Manual: http://www.ks.uiuc.edu/Research/namd/current/ug/
- Downloads: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
- Tutorials: http://www.ks.uiuc.edu/Training/Tutorials/
A registration required to download software.
Release notes:
- Version 2.11: http://www.ks.uiuc.edu/Research/namd/2.11/notes.html
NAMD Wiki, How to compile: https://proteusmaster.urcf.drexel.edu/urcfwiki/index.php/Compiling_NAMD
Strengths
Weak points
GPU support
Quickstart Guide
This section summarizes configuration details.
Environment Modules
The following modules providing NAMD are available on graham and cedar.
Compiled without CUDA support:
- namd-multicore/2.12
- namd-verbs/2.12
Compiled with CUDA support:
- namd-multicore/2.12
- namd-verbs-smp/2.12
To access these modules which require CUDA, first execute:
module load cuda/8.0.44
Note: using verbs library is more efficient than using OpenMPI, hence only verbs versions are provided.
Submission Scripts
Please refer to the page "Running jobs" for help on using the SLURM workload manager.
Serial Job
Here's a simple job script for serial simulation:
#!/bin/bash
#SBATCH --time 0:30 # time (D-HH:MM)
module load namd