DL_POLY is a general purpose molecular dynamics simulation tool developed and provisioned for UK academia. You can read more about it on the DL_POLY web page.
To access this software you need to agree to the license terms, please submit a request to the Research Computing team via our contact form confirming you accept the license terms and wish to be added to the DL_POLY user group.
The licence terms are available on the DLpoly license page.
Loading the module#
DL_POLY versions 4.08 and 4.09 are currently available on ARC3 and 4.09 and 4.10 on ARC4. You can add the DL_POLY module by using a command like this:
$ module add dl_poly/4.09
This adds the DL_POLY 4.09 executable files to your environment and must be included in your job submission script to ensure your jobs can also access DL_POLY.
DL_POLY 4.09/4.10 is built with to both run in serial and in parallel depending
on the resources available using the single executable
An example job submission script that calls DLpoly is shown below:
#$ -cwd -V #$ -l h_rt=48:00:00 #$ -pe ib 16 module add dl_poly/4.10 mpirun -np $NSLOTS DLPOLY.Z
This requests 48 hours of runtime on 16 processes spread over Infiniband. Saved as dlpoly.sh this can be submitted to the queue with the command:
$ qsub dlpoly.sh
DL_POLY can be run in serial using the same executable without prepending the
#$ -cwd -V #$ -l h_rt=48:00:00 module add dl_poly/4.10 DLPOLY.Z
To submit the above script do:
$ qsub dlpoly_serial.sh
Version 4.08 is built on ARC3 and has a slightly different executable that can be used as follows:
Job submission example#
An example job submission script that calls to the
executable and requests multiple cores over Infiniband.
#$ -cwd -V #$ -l h_rt=48:00:00 #$ -pe ib 16 module add dl_poly/4.08 mpirun DLPOLY.Z.parallel
The same executable can also be used to run a job in serial.