DL_POLY

DL_POLY is a general purpose molecular dynamics simulation package. The installation of DL_POLY on the henry2 cluster was compiled using the Intel 8.1 compiler with MPICH library to run in parallel on the cluster. DL_POLY license is a no-fee academic license (see terms at bottom of page).

There are two versions of DL_POLY. Version 2 was parallelized using replicated storage and is appropriate for use on problems with up to about 30,000 atoms. Version 3 uses domain decomposition (distributes storage requirements across parallel tasks) and can handle approximately 1 million atoms.

DL_POLY versions 2.16 and 3.06 are installed on henry2 under /usr/local/apps/dl_poly_2.16 and /usr/local/apps/dl_poly_3.06 respectively. Users with tcsh as their default shell can set up their environment to run DL_POLY with the command ‘add dl_poly_2’ or ‘add dl_poly_3’ for DL_POLY version 2 or 3 respectively.

Additional information about using DL_POLY is available from the DL_POLY web site.

To run a DLPOLY job Create a file – say it is named run_dlpoly – that contains the lines:

The current directory should also include the files FIELD, CONTROL, and CONFIG (see the link above for how to construct these). In the current terminal session, type:

The above file btry asks for 4 processors and ten minutes. Typically a dl_poly_3 job will require more resources than that, but running with four or fewer processors for fifteen minutes gives the job “debug” priority, so it executes more or less real time and you can catch mistakes before going on to a real job submission which will perhaps queue for several hours and then run for several hours. The command “add dl_poly_3” is required only once in a terminal session.

See the DL_POLY web site for more information on using DL_POLY.

License terms

DL_POLY is licensed for academic purposes which the license defines as “fundamental or basic research or academic teaching, including any fundamental research that is funded by any public or charitable body, but not any purpose that generates revenue (as opposed to grant income) for the licensee or any third party. Any research that is wholly or partially sponsored by any profit making organisation or that is carried out for the benefit of any profit-making organisation is not an Academic Purpose.”