The simulation consists of particles diffusing inside a cylindrical nanopore. The surface of the nanopore is covered with adsorbing sites, and the particles reversibly adsorb at the inner surface of the nanopore. The adsorption/desorption processes are modelled using bond/create and bond/break commands respectively. A bond forms if a particle comes close enough to a trap. An additional harmonic potential is added to trapped particles. The wall of the cylinder is modelled using the wall/region command. This video has been made with this script.
Run the input.lammps script using LAMMPS. If you are new to LAMMPS and VMD, you can find tutorials and instructions here.
If you are new to LAMMPS, you can find tutorials and instructions here.
Feel free to contact me by email if you have inquiries. You can find contact details on my personal page.
If you use this script, please cite Gravelle, Netz, Bocquet, Adsorption Kinetics in Open Nanopores as a Source of Low-Frequency Noise, Nano Lett. 2019, 19, 10, 7265–7272