RCC is intensively supporting research using molecular simulations through access to UQ’s high-performance computer facilities, software purchases, licences and software installation support and through a RCC specialist in molecular simulations.
Molecular modelling looks at the detailed interaction of atoms and molecules. For most systems of interest this requires specialised software and large high-performance computer (HPC) clusters.
While there are many different software available, they all use an atomistic level description of the system where the smallest unit might be an atom (molecular dynamics) or the electrons of each atom (quantum dynamics).
Molecular simulations are used in computational chemistry, drug design, computational biology and materials design.
Molecular dynamics (MD) software supported by RCC include Gromacs, NAMD and LAMMPS, which are free of charge and part of the standard install packages. MD is traditionally applied to problems in material science, biochemistry and biophysics.
MD software traditionally uses MPI (Message Passing Interface) and scales to a large number of cores. This type of software is therefore particularly suited to UQ’s Tinaroo HPC cluster.
In a recent move, RCC purchased a UQ licence of Amber 18. Amber software proved to be particularity suited to Graphics Processing Unit (GPU) architectures and has been installed on UQ’s new GPU HPC cluster Wiener. (Read the case study about this.)
RCC’s purchase of software site licences for UQ as a whole means more of the university’s researchers will have access to the software, and will have the support of RCC’s technical team. RCC also installs the software on the appropriate UQ HPC cluster, such as Tinaroo, FlashLite, Awoonga or Wiener, making it even easier for researchers to use the software. RCC will also support UQ systems administrators to install the software on local servers, enhancing the software’s availability.
Quantum dynamics (often denoted as quantum mechanics, QM) is traditionally applied to problems in chemistry, physics, biology and materials science; mainly problems where quantum effects play an important role or where knowledge on bond formation and breaking is required.
Quantum dynamics software includes Gaussian, ORCA, VASP, Quantum ESPRESSO and CP2K. ORCA, Quantum ESPRESSO and CP2K are free software, while Gaussian and VASP require the purchase of a licence. RCC is in the process of acquiring a HPC licence for VASP, which will enable RCC staff to install the newest versions on UQ machines and make VASP readily available to the university’s researchers who have a valid user licence
CP2K is part of the standard packages installed but, like the others listed above, is also supported through custom installed versions.
ORCA is a recent addition to RCC’s supported software. It is used to simulate molecules and uses MPI, so is suited to HPC Tinaroo. However, HPC FlashLite is also suitable for those calculations that involve large amounts of temporary files. (Read the case study about this.)
RCC has traditionally supported Gaussian, one of the most used quantum dynamics software. RCC purchased and installed G09, the currently available version, as a UQ site licence, which makes it not only available on the HPC clusters, but also allows users to install it on local servers.
Due to the wide usage of Gaussian across disciplines, RCC has recently purchased the latest version, G16, and also Gaussian’s graphical interface, GaussView, as a UQ site licence for the first time. This will enable researchers to build their models, set up their calculations and analyse their Gaussian results from their desktop or local servers. This will enable new or less experienced users to use Gaussian for their research for the first time. (Read the two case studies about this, one featuring Dr Elizabeth Krenske, the other, Dr Robert Reid.)
With RCC’s software purchases and technical support, UQ’s molecular dynamics and quantum dynamics researchers are better positioned to make even bigger discoveries.
UQ researchers using any of the software packages mentioned in this article can contact RCC’s specialist in molecular simulations, Dr Marlies Hankel, if they experience issues with the software. Marlies is a computational scientist with a background in mathematics, programming, quantum molecular dynamics and HPC cluster management. Email: m.hankel@uq.edu.au.
Marlies will chair the Molecular Simulation Workshop on Wednesday, 1 August at UQ St Lucia. The workshop, which is open to all researchers, will provide entry-level introductions to Gaussian, VASP, Gromacs, Amber and LAMMPS. Register for this workshop by Friday, 13 July (more information).
For HPC queries or issues, please contact the RCC Support Desk: rcc-support@uq.edu.au.
