OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

We present a simple model for the discrepancy in the coverage of a gold (111) surface by two silicon phthalocyanines. The model involves random sequential adsorption (RSA) simulations with two different landing molecules, one of which is tilted relative to the substrate surface and can (under certain conditions) allow neighboring molecules to overlap. This results in a jamming limit that is near full coverage of the surface. The nonoverlapping molecules reproduce the half-monolayer jamming limit that is common in continuum RSA models with ellipsoidal landers. Additionally, the overlapping molecules exhibit orientational correlation and orientational domain formation evolving out of a purely random adsorption process.