Computational methods are increasingly being used for modeling the self-assembly process of nanoparticles. For efficiency and cost-effectiveness purposes, coarse-grain and multi-scale models are generally used. Nowadays, the recent advances in computation algorithms, especially in GPU-based computation, allow the use of all-atom representations of the system and expand significantly the scope of these atomistic simulations. We will present the evaluation of several all-atom force fields (CGenFF/CHARMM, GAFF/AMBER and OPLS-AA) for their ability to model the self-assembly of different nanoparticles. The influence of different factors (size of the system, relative ratio of the components, etc.) on the simulation outcome will be shown, and a comparison with united-atom (GROMOS) or coarse-grain (MARTINI) force fields will be provided to complete the global picture. We will highlight the advantages and limitations of each approach, as well as the potential applications in modeling the drug delivery process. Overall, our results are in agreement with a better description of the simulation systems by the all-atom force fields, but at the cost of significantly higher computational resources requirements.

Use of atomistic molecular dynamics simulations for in silico self-assembly of nanoparticles: Opportunities and limitations

256th National Meeting (2018)

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