The HECToR Service is now closed and has been superceded by ARCHER.


Licensing and access

NAMD is licensed software that is free for non-commercial use. You can read the licence. All HECToR users have access to the NAMD binaries.



To run NAMD you need to add the correct module to your environment. The default version of NAMD on HECToR is currently 2.7 so

module add namd

will give you access to NAMD 2.7. If you want NAMD 2.9, you should use the command 'module add namd/2.9'.

The NAMD executable is called namd2.

Example job submission script

#!/bin/bash --login
#PBS -N namd_job
#PBS -l mppwidth=2048
#PBS -l mppnppn=32
#PBS -l walltime=03:00:00
# Change this to your own budget
#PBS -A z01

# Move to directory that script was submitted from
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)

# Set the number of threads to 1
#   This prevents any system libraries from automatically 
#   using threading.

module add namd/2.9

# you should replace "input.namd" in the line below with your input filename
aprun -n 2048 namd2 input.namd

Useful links