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
simulations for practitioners. The web interface makes it possible for experts to build a rich
library of simulation components and for ordinary users to create full simulations by param-
eterizing and composing the components. A visual programming interface makes it possible
to create optimization workflows where the simulators are invoked multiple times with various
parameter configurations based on results of earlier simulation runs. Simulation configurations
including the various parameters, the version of tools utilized and the results are stored in a
database to support searching and browsing of existing simulation outputs and facilitating the
reproducibility of scientific results.