NAMD
NAMD is a molecular dynamics program designed for parallel computation. Full and efficient treatment of electrostatic and van der Waals interactions are provided via the Particle Mesh Ewald algorithm. NAMD interoperates with CHARMM and X-PLOR as it uses the same force field and includes a rich set of MD features (multiple time stepping, constraints, and dissipative dynamics).
NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License.
Availability / Target HPC systems
We are currently in the process of providing modules on Woody, TinyGPU, and Emmy. All these modules will be based on pre-built official binaries distributed by the developers of NAMD.
There will be no NAMD module on Meggie for the time being.
Notes
none yet
Sample job scripts
serial job on Woody
#!/bin/bash -l #PBS -lnodes=1:ppn=4,walltime=01:00:00 #PBS -N name cd $PBS_O_WORKDIR module load namd/2.14-multicore namd2 +p4 input.conf > logfile
parallel job on Emmy
#!/bin/bash -l #PBS -lnodes=2:ppn=40,walltime=01:00:00 #PBS -N name cd $PBS_O_WORKDIR module load namd/2.14-verbs-smp PPN=40 namd2 +p$PPN +idlepoll ++ppn $PPN input.conf > logfile
single GPU job on TinyGPU
#!/bin/bash -l #PBS -lnodes=1:ppn=4:v100:smt,walltime=01:00:00 #PBS -N name cd $PBS_O_WORKDIR module load namd/2.14-multicore-cuda namd2 +p8 input.conf > logfile
Further information
- http://www.ks.uiuc.edu/Research/namd/
- http://www.ks.uiuc.edu/Research/namd/2.14/ug/
- https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/
Mentors
- Dr. A. Kahler, RRZE, hpc-support@fau.de
- AG P. Imhof (Computer Chemistry Center)