  Molecular dynamics (MD) simulations enable the description of ma- terial
properties and processes with atomistic detail by numerically solv- ing the
time evolution of every atom in the system. We introduce Poly- merModeler, a
general-purpose, online simulation tool to build atomistic structures of
amorphous polymers and perform MD simulations on the re- sulting configurations
to predict their thermo-mechanical properties. Poly- merModeler is available,
free of charge, at nanoHUB.org via an interactive web interface, and the actual
simulations are performed in the cloud us- ing nanoHUB.org resources. Starting
from the specification of one or more monomers PolymerModeler builds the
polymer chains into a simulation cell with periodic boundary conditions at the
desired density. Monomers are added sequentially using the continuous
configuration bias direct Monte Carlo method, and copolymers can be created
describing the desired se- quence of monomers. PolymerModeler also enables
users to perform MD simulations on the structures created by the builder using
the Dreiding force field and Gasteiger partial atomic charges. We describe the
force field im- plementation and the various options for the MD simulations
that use the LAMMPS simulator. PolymerModeler MD simulations for a PMMA sam-
ple show good structural agreement with experiments and are in good agree- ment
with simulations obtained with commercial software.
