Dear all,
I am running a MD simulation of polystyrene with AMBER. It looks the benzene ring on the backbone distribute evenly. My advisor asked me to find a way to evaluate the behavior of the change of ring structure on the polymer. Does anyone have any idea about this?
Thanks,
X Sun.
In this case, you should calculate Radial Distribution Function (RDF). Based the RDF results you can analyze most probable position between two molecule or atoms.
Check this out, you will find this paper useful:
https://www.researchgate.net/publication/216456719_Propanepropylene_diffusion_in_zeolites_Framework_dynamics?ev=prf_pub
The FF is not a problem, AMBER is optimized for Hydrocarbons, so your pretty safe using this FF.
Article Propane/Propylene Diffusion in Zeolites: Framework Dynamics
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