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 & Restrictions
NAMD is available without restriction to all OSC users.
The following versions of NAMD are available:
*: Current default version
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