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.
Availability and Restrictions
The following versions of NAMD are available:
You can use
module spider namd to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
NAMD is available without restriction to all OSC users.
To load the NAMD software on the system, use the following command:
module load namd/"version" where "version" is the version of NAMD you require. The following will load the default or latest version of NAMD:
module load namd.
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 Oakley below demonstrates some important points. It requests 24 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=12 #PBS -l walltime=2:00:00 #PBS -S /bin/bash #PBS -j oe module load namd 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
We have GPU support with NAMD 2.12 for Owens and Ruby clusters, and with NAMD 2.11 for Oakley. These temporarily use pre-compiled binaries due to installation issues. For more detail, please read the corresponding example script:
~srb/workshops/compchem/namd/apoa1.namd212nativecuda.owens.pbs # for Owens ~srb/workshops/compchem/namd/apoa1.namd212nativecuda.ruby.pbs # for Ruby ~srb/workshops/compchem/namd/apoa1.namd211nativecuda.oakley.pbs # for Oakley