NAMD

Useful links

Licensing and access

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

Running

Running on ARCHER

To run NAMD you need to add the correct module to your environment:

module add namd

Will give you access to the NAMD executable, called namd2.

Example job submission script

#!/bin/bash --login
#PBS -N namd_job

# Select 128 nodes (maximum of 3072 cores)
#PBS -l select=128

#PBS -l walltime=0:20:0

# Change this to your own budget code
#PBS -A budget

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

module add namd

# you should replace "input.namd" in the line below with your input filename
aprun -n 3072 namd2 input.namd

Running on ARCHER KNL

Instructions for running NAMD on the ARCHER KNL system can be found on GitHub at:

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