I need to do molecular dynamics simulation of cyclodextrine molecules for a project and I am searching for an open source solution that can be used. I found LAMMPS to be quite well maintained and wanted to use it for the MD simulation. However, after spending now around 10 hours trying to figure out how to specify an input geometry for a LAMMPS calculation, I am stuck. Has anyone experience with doing MD simulations of molecules using LAMMPS? Given an input structure in standard .xyz format, how do I start a LAMMPS MD calculation on it?