Valinomycin/Membrane Simulation Detail from a DL_POLY simulation
is a general purpose molecular dynamics simulation package
developed at STFC
W. Smith, T.R. Forester and I.T. Todorov. The package was
developed under the auspices of the Engineering and Physical
Sciences Research Council (EPSRC
for the EPSRC’s Collaborative Computational Project for
the Computer Simulation of Condensed Phases
the Computational Chemistry Group
) at Daresbury
Laboratory and the Natural Environment Research Council
) for the NERC’s
eScience project Computational Chemistry in the
DL_POLY can be used to simulate a wide variety of molecular systems including:
- Simple atomic systems and mixtures, e.g. Ne, Ar, Kr, etc.
- Simple unpolarisable point ions, e.g. NaCl, KCl, etc.
- Polarisable point ions and molecules, e.g. MgO, H2O etc.
- Polymers with rigid bonds, e.g. CnH2n+2
- Polymers with rigid bonds and point charges, e.g. proteins, macromolecules etc.
- Silicate glasses and zeolites
- Simple metals and metal alloys, e.g. Al, Ni, Cu, Cu3Au etc.
- Hydro-carbons and transition elements, e.g. C, Si, Ge, SiC, SiGe, ets.
There are two versions of DL_POLY packages - DL_POLY_2 and DL_POLY_3.
They are written in modularised, free formatted F90 (+MPI) with rigorous
code syntax (FORCHECK and NAGWare verified) and no external library dependencies.
Both versions use MPI1.1 for interprocessor communication. However,
the most up-to-date version of DL_POLY_3 requires MPI-I/O (MPI2) for its
parallel printing functionality.
Although both versions serve the same purpose, they implement
parallelisation in a different manner. This ultimately leads to difference
in performance with regard to system size and complexity between the
two vesrions as well as some differences in functionality due to the
specificity of the technical constraints in either parallelisation strategy.
A summary of the major differences between DL_POLY_2 and DL_POLY_3 is
DL_POLY_2 (version 18)
- Replicated Data parallelisation (algorithmic), limits up to 30,000
atoms with good parallelisation up to 32/64 (system dependent) processors
(with no restriction on the processor count)
- Full force field and molecular description
- Features not ported from DL_POLY_3:
- Andersen, Langevin and Martina-Tuckerman-Klein ensembles
- variable timestep
- defects detection
- system replication
- full exlectrostatics exclusion
- RDF lookup specification in FIELD
DL_POLY_3 (version 09)
- Domain Decomposition parallelisation (spatial), limits up to 2.1*109
atoms with inherent parallelisation (to any high processor count, N
as long as the system can be distrubuted equi-spatially well on N = k * l * m,
if SPM Electrostics is used N is restricted to the power of 2 series)
- Full force field and molecular description but no rigid bodies
- Features not ported from DL_POLY_2:
- Truncated octahedral (IMCON=4), Rhombic dodecahedral (IMCON=5) and
Hexagonal prism (IMCON=7) periodic boundaries
- Hautman-Klein (z-dimention aperiodic) Electrosatics
Restarting simulations between DL_POLY_2 and DL_POLY_3 is not possible!
However, either package will handle the other's input with the exception
of cases when a non-ported feature is used.
Accessing DL_POLY on the HPCx system
Please note that the source code for the package is not publicly
available on the machine but is available to each individual researcher
under a licence. In order to run DL_POLY on HPCx you will need to
apply for a DL_POLY licence. If you require a licence then visit
the DL_POLY official webpage.
DL_POLY_2 executable is named DLPOLY.X whereas
DL_POLY_3 one DLPOLY.Y. As either executable is available
only in parallel mode it can be invoked on nproc
processors using the poe command as shown below:
poe -procs <nproc> /usr/local/packages/dlpoly/DLPOLY.Z
This is avalable through the
DL_POLY official webpage
which contains links to
- DL_POLY FAQ Section (basic how-tos)
- DL_POLY Java GUI (available under the standard release
to help visualise structures, prepare input files and analyse
- DL_POLY Manuals (self-referencing PDF documents)
- DL_POLY On-line Licensing (terms)
- DL_POLY On-line Forum (discussion board facility to post
scientific, engineering and general help questions and answers
on DL_POLY codes and simulations)
- DL_POLY Benchmark Reports
- DL_POLY Tutorial
- DL_POLY Exercises
- Past DL_POLY Mail Shots
contact email -
© UoE HPCX Ltd