So I thought I'd upload a few videos of a recent MD simulation that is part of some work I'm doing in collaboration with a colleague at the University of Western Australia. A quick summary:

60 Benzene molecules in a box 120 Å x 120 Å x 120 Å.
Simulation begins at 1000K for 200 ps then drops to 100K for the remaining 3 ns.
Uses the LAMMPS MD code developed at Sandia Labs, US.
Interactions governed by the All-Atoms OPLS potential (more about this and it's implementation in a future post)
Videos below are produced with the visualisation software AVAS.

Close up view of the final stages of cluster formation:

VIDEO: Molecular Dynamics Simulation of the Clustering of Polycyclic Aromatic Hydrocarbons

Videos of Benzene clustering at 100K using LAMMPS and OPLS-AA

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