Our group develops various scientific software and simulation packages.
The LAMMPS code is one of the standard materials modelling simulation packages used at many high performance computing facilities around the world. It has a global user community in the thousands and underpins countless research projects across a wide variety of scientific disciplines.
We develop the LAMMPS implementation of the oxDNA coarse-grained model of DNA and RNA [1-4]. The code is provided as optional CG-DNA package and is available from the central repository of the LAMMPS organisation. The latest development that is not yet part of a stable release is available from our LAMMPS fork on GitHub.
We contribute to the development and extension of tacoxDNA [5], the suite of tools and converters for the oxDNA coarse-grained DNA models. tacoxDNA is available as standalone code and through a web server.
Ludwig is a software package for simulation of soft matter and complex fluids. The package takes its name from Ludwig Boltzmann as it uses the lattice-Boltzmann method for solving the Navier-Stokes equation of hydrodynamics. It is also possible to combine the lattice-Boltzmann method with a range of other methods for simulation of complex fluid systems such as free-energy methods.
Ludwig can be deployed on diverse computing architectures including multi- and many-core processors as well as general purpose graphics processing units (GPUs). Ludwig is open source software and available from our repository at GitHub.
[1] T. E. Ouldridge, A. A. Louis, J. P. K. Doye, J. Chem. Phys 134, 085101 (2011).
[2] P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014).
[3] B.E. Snodin, F. Randisi, M. Mosayebi, P. Šulc, et al., J. Chem. Phys.142, 234901 (2015).
[4] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
[5] A. Suma, E. Poppleton, M. Matthies, P. Šulc, et al., J. Comput. Chem. 40, 2586–2595 (2019).
Soft Matter and Biophysics 