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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

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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

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Required modules

1. CPU version
   1. intel/20.0.3
   2. mvapich2/2.3.4 OR mpich/3.3.2
2. GPU version
   1. intel/19.0.3
   2. cuda/10.2.89
   3. mvapich2/2.3.4 OR mpich/3.3.2

Usage: srun $(which namd2) <input file> > <output file>
Alternate Usage: $(which charmrun) +p$SLURM_NTASKS $(which namd2) <input file> > <output file>

Links

For more information visit https://www.ks.uiuc.edu/Research/namd/

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