NAMD

License Arrangements

This software is installed with a non-commercial use license. Access to this software is restricted. User must agree to the license, found here. Please send a written statement accepting the license terms as a ticket to the Research Computing Team in order for us to give you access to NAMD.

Example submission script

An example script, namdexample.sh , looks like:

#!/bin/bash
# Request 8 cores anywhere on the compute nodes
#$ -pe ib 8
# Run for at most 12 hours
#$ -l h_rt=12:0:0
# Reserve 1Gbyte of RAM
#$ -l h_vmem=1G
# Run in the current directory
#$ -cwd

module add namd/2.13
mpirun namd2 name_of_config_file.conf > output_log_file.log

This example requests 8 cores for 12 hours, with each core limited to 1Gb of RAM. It assumes that you are submitting the job from the directory containing your input files.

Note

Prior to NAMD 2.9, the namd2 MPI binary was called namd2.MPI.

Example GPU submission script

You may want to run using GPUs where you are likely to see a considerable speedup.

#!/bin/bash
# Run for at most 12 hours
#$ -l h_rt=12:0:0
# Request a GPU (in this case a v100)
#$ -l coproc_v100=1
# Run in the current directory
#$ -cwd

module add namd/2.13gpu
namd2 +idlepoll +p${NSLOTS} name_of_config_file.conf > output_log_file.log

This example requests 1 GPU, which comes with 1/4 of the resources available on the machine - in this case that means 10 cores and 48Gbytes of RAM. It assumes that you are submitting the job from the directory containing your input files.