ICHEC Software
Information about software packages installed on the ICHEC systems.
NAMD
Versions Installed
Stokes: 2.7b2 / 2.7b3(default) / 2.8b1 / 2.9
Stoney: 2.7b2
Description
NAMD is a molecular dynamics application designed specifically for the simulation of large biomolecular systems using modern parallel architectures. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign using object-oriented techniques. NAMD can read X-PLOR, CHARMM, AMBER, and GROMACS input files.
NAMD only uses the GPU for nonbonded force evaluation. Energy evaluation is done on the CPU. To benefit from GPU acceleration you should set outputEnergies to 100 or higher in the simulation config file. Some features are unavailable in CUDA builds, including alchemical free energy perturbation. As this is a new feature you are encouraged to test all simulations before beginning production runs. Forces evaluated on the GPU differ slightly from a CPU-only calculation, an effect more visible in reported scalar pressure values than in energies.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
License
The NAMD package is available for use by all ICHEC users. Contact the Helpdesk to gain access to this package.
Additional Notes
The NAMD package is installed under /ichec/packages/namd/ and an environment module is available for it:
To run NAMD follow this example:
#!/bin/bash
#PBS -N JobName
#PBS -A ngche005b
#PBS -r n
#PBS -l nodes=2:ppn=12,walltime=24:00:00
cd $PBS_O_WORKDIR
module load namd
namd2=`which namd2`
mpiexec_mpt $namd2 InpFile > OutFile
To run NAMD with CUDA support on Stoney follow this example:
#!/bin/bash
#PBS -N JobName
#PBS -A ngche005b
#PBS -q GpuQ
#PBS -r n
#PBS -l nodes=2:ppn=12,walltime=24:00:00
cd $PBS_O_WORKDIR
module purge
module load gcc cuda/4.0 mvapich2-gnu namd/2.8
cmd="namd2 +idlepoll src/alanin"
mpiexec -np 2 $cmd
The NAMD user guide is available from the NAMD webpage.