Molecular dynamics (MD) simulations play an important role in materials design. However,
the effective use of the most widely used MD simulators require significant expertise of the
scientific domain and deep knowledge of the given software tool itself. In this paper, we present
a tool that offers an intuitive, component-oriented approach to design complex molecular sys-
tems and set up initial conditions of the simulations. We integrate this tool into a web- and
cloud-based software infrastructure, called MetaMDS, that lowers the barrier of entry into MD