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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| Version | module name |
|---|---|
| 2.14 | namd/2.14 |
| 2.14 | namd/2. |
...
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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| 14-gpu |
| Code Block | ||
|---|---|---|
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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/
