About Ångström-dimer

Ångström-dimer is a molecular modelling software to study the dynamics of Ångström-scale chemically powered self-propelled motors (Colberg and Kapral 2014, Colberg and Kapral (2015)). The software uses molecular dynamics to simulate the molecular motion of a single to tens of sphere-dimer motors in an explicit Lennard-Jones solvent comprising on the order of 100,000 particles.

Ångström-dimer relies on novel computational techniques to scale from a multi-core processor to a parallel accelerator with thousands of scalar cores. The simulation algorithms are composed in the OpenCL C language using run-time code generation, which allows running simulations with optimal efficiency across a variety of devices, such as AMD GPUs, NVIDIA GPUs, and Intel CPUs.

A simulation is orchestrated using Lua scripts run with LuaJIT, an interpreter and tracing just-in-time compiler for the Lua language that provides native C data structures through its foreign function interface (FFI). Particle trajectories of nanomotors and solvent, and a versatile set of structural and dynamical observables are stored in an H5MD file, a file format for molecular data (Buyl, Colberg, and Höfling 2014) based on the hierarchical data format (HDF5).

References

Buyl, Pierre de, Peter H. Colberg, and Felix Höfling. 2014. “H5MD: A Structured, Efficient, and Portable File Format for Molecular Data.” Computer Physics Communications 185 (6): 1546–53. doi:10.1016/j.cpc.2014.01.018.

Colberg, Peter H., and Raymond Kapral. 2014. “Ångström-Scale Chemically Powered Motors.” EPL 106 (3): 30004. doi:10.1209/0295-5075/106/30004.

———. 2015. “Nanoconfined Catalytic Ångström-Size Motors.” J. Chem. Phys. 143: 184906. doi:10.1063/1.4935173.