namd
Link to section 'Description' of 'namd' Description
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. 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.
Link to section 'Versions' of 'namd' Versions
- Scholar: 2.13-multinode, 2.13-singlenode, 3.0-alpha3-singlenode
- Gilbreth: 2.13-multinode, 2.13-singlenode, 3.0-alpha3-singlenode
- Anvil: 2.13-multinode, 2.13-singlenode, 3.0-alpha3-singlenode
Link to section 'Module' of 'namd' Module
You can load the modules by:
module load ngc
module load namd
Link to section 'Example job' of 'namd' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run namd on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --gpus-per-node=1
#SBATCH --job-name=namd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml ngc namd