LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator.
Molecular Dynamics is a method of computer simulation enabling us to see and study physical movements of atoms and bigger molecules, which are allowed to interact between themselves for a fixed period of time, so evolution of the system over time can be seen – we’ll see behavior of molecules under conditions chosen for our simulation. LAMMPS is based on Classical Mechanics theory, so at lower level it integrates Newton’s equations of motion of collection of molecules, of which we have built our model for exact simulation. Those particles will interact via short-range or long-range forces. Certain initial and boundary conditions can be provided for our simulation, which will govern motion of molecules. In LAMMPS we mostly simulate aggregates of thousands or millions of atoms. Hence, this is a good method for investigating numerous physical characteristics of nanoparticles and a realistics approximation of macro properties.
Two movies are available (described in the above text of Szymon): wygrzewanie_C_nonperiodic.mp4 and bombardowanie_C.mp4
The code for interlayer potential of graphene introduced by Lebedeva et al., implemented in official stable version of LAMMPS.
A lecture during Festive of Science 2018 in Warsaw, somewhat related to Molecular Dynamics (in Polish): O bogactwie własności grafenu i innych materiałów dwuwymiarowych.