Attention

WARNING: From 8am on 30th June until 5pm on 4th July 2025, there will be no access to the Stanage HPC cluster.

We will try to minimise this downtime and it is possible that Stanage will return to service before 4th July. We will notify you by email when Stanage is back online and available for job submission.

DL_POLY_4

DL_POLY_4 is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov, W. Smith, A.M. Elena and others.

Interactive Usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

The latest version of DL_POLY_4 (currently version 5.0.0) is made available with the command:

$ module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b

After this the DL_POLY_4 command can be run from the terminal prompt

Batch Usage

Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, to run DLPOLY.Z and which is submitted to the queue by typing sbatch my_job.sh.

#!/bin/bash
#SBATCH --job-name=DL_POLY_4_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --mem=2000
#SBATCH --time=00:30:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL

module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b
# Get Example 2 from the DL_POLY website.
# ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Tutorial_Notes.pdf
wget ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Exercise2.tar.gz
tar -xvf Exercise2.tar.gz
cd Exercise2
mpirun -np $SLURM_NTASKS DLPOLY.Z

Installation notes

Installation method

DL_POLY_4 version 5.0.0 was installed using Easybuild 4.4.0 and was optionally interfaced with the PLUMED 2.6.2 library. build details can be found in /usr/local/packages/live/eb/DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b/easybuild

Installation was tested as with the above batch script with example 2 directly taken from ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/) with the following decomposeParDict: https://openfoamwiki.net/index.php/DecomposePar