NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.
NAMD is available without restriction to all OSC users.
The following versions of NAMD are available:
To load the NAMD software on the Glenn system, use the following command:
module load namd-2.6-mpi
To load the latest NAMD software on the Oakley system, use the following command:
module load namd/2.11
NAMD is rarely executed interactively because preparation for simulations is typically performed with extraneous tools, such as, VMD.
Sample batch scripts and input files are available here:
The simple batch script for Glenn below demonstrates some important points. It requests 16 processors and 2 hours of walltime. If the job goes beyond 2 hours, the job would be terminated.
#PBS -N apoa1 #PBS -l nodes=2:ppn=8 #PBS -l walltime=2:00:00 #PBS -S /bin/bash #PBS -j oe module load namd-2.6-mpi cd $PBS_O_WORKDIR pbsdcp -p apoa1.namd apoa1.pdb apoa1.psf *.xplor $TMPDIR cd $TMPDIR run_namd apoa1.namd pbsdcp -pg '*' $PBS_O_WORKDIR
The NAND users group on Armstrong