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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