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.
Usage
Add module: module load namd/2.11
Dependent modules loaded: fftw, mvapich2 and intel
Usage: srun $(which namd2) <input file> > <output file>
Alternate Usage: mpiexec -n $SLURM_NTASKS -f $SLURM_NODEFILE $(which namd2) <input file> > <output file>
Alternate Usage: mpirun_rsh -export -n $SLURM_NTASKS -hostfile $SLURM_NODEFILE $(which namd2) <input file> > <output file>
Alternate Usage: $(which charmrun) +p$SLURM_NTASKS $(which namd2) <input file> > <output file>
Absolute path to namd executable: /share/Apps/namd/2.11/bin/namd2
Absolute path to charmrun executable: /share/Apps/namd/2.11/bin/charmrun
To obtain the SLURM_NODEFILE variable, add the following to your submit script
export SLURM_NODEFILE=$(get_slurm_nodelist)