NAMD is a powerful molecular dynamics program design to simulate large biomolecular systems in a manner which is scalable across large numbers of processors.
Using NAMD on RCC Resources
NAMD is available on the HPC and Spear using the Intel Compilers and MVAPICHv2. It automatically receives the number of processors you wish to run on when you submit NAMD jobs via the Slurm Scheduler. This version also interprets TCL commands in configuration files.
The binary executable for namd is available at the following filesystem location:
To submit NAMD jobs to Slurm, refer to the following example submission script:
#!/bin/bash #SBATCH -N 8 #SBATCH --job-name="namd" #MOAB -t 10:00:00 cat $SLURM_JOB_NODELIST module load intel-mvapich2 export NAMD=/opt/hpc/intel/mvapich2/bin cd $SLURM_SUBMIT_DIR pwd srun $NAMD/namd2 CONFIG.namd +isomalloc_sync > namd.`date +%Y%m%d.%H%M%S`.log