NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit Ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
Restricted Software: You must agree to the NAMD User License Conditions before you can gain access to the NAMD software.
To run a NAMD job in parallel, please use the following template as an example:
#!/bin/csh #$ -pe mpi-12 24 #$ -m ae #$ -M firstname.lastname@example.org #$ -q long module load namd # load NAMD module mpirun -np $NSLOTS namd2 ./config-file
User License Restrictions
Before you can be granted access to the NAMD software, please review the following user license conditions. Once you have read and agreed to the conditions please email CRC Support with your confirmation, after which you will be added to the NAMD software access group.
- See the official website: NAMD