About nano-dimer

Nano-dimer is a molecular modelling software to study the dynamics of chemically powered self-propelled nanomotors (Kapral 2013). The software combines molecular dynamics and multi-particle collision dynamics (Malevanets and Kapral 1999; Malevanets and Kapral 2000; Ihle and Kroll 2001) to simulate the molecular motion of a single to hundreds of sphere-dimer motors (Rückner and Kapral 2007) and their long-range hydrodynamic interaction in a solvent comprising several million particles.

Nano-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.

Ihle, T., and D. M. Kroll. 2001. “Stochastic Rotation Dynamics: A Galilean-Invariant Mesoscopic Model for Fluid Flow.” Phys. Rev. E 63: 020201. doi:10.1103/PhysRevE.63.020201.

Kapral, Raymond. 2013. “Perspective: Nanomotors Without Moving Parts That Propel Themselves in Solution.” Journal of Chemical Physics 138 (2): 020901. doi:10.1063/1.4773981.

Malevanets, Anatoly, and Raymond Kapral. 1999. “Mesoscopic Model for Solvent Dynamics.” Journal of Chemical Physics 110 (17): 8605–13. doi:10.1063/1.478857.

———. 2000. “Solute Molecular Dynamics in a Mesoscale Solvent.” Journal of Chemical Physics 112 (16): 7260–9. doi:10.1063/1.481289.

Rückner, Gunnar, and Raymond Kapral. 2007. “Chemically Powered Nanodimers.” Phys. Rev. Lett. 98 (15): 150603. doi:10.1103/PhysRevLett.98.150603.