Accelerated Atomistic Simulations of a Supramolecular Polymer in Water

Davide Bochicchio; Giovanni M. Pavan

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arXiv · 1803.10491

Accelerated Atomistic Simulations of a Supramolecular Polymer in Water

Davide Bochicchio·Giovanni M. Pavan

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Abstract

All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a reliable equilibrated configuration for these soft assemblies in aqueous solution remains a challenging task mainly due to the complexity of the atomistic systems and the long simulation time needed for their equilibration. Here we have tested two well-known advanced simulation methods (Accelerated Molecular Dynamics and Metadynamics) on an atomistic model of water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer and have compared the obtained data to classical molecular dynamics. Our results show that both techniques can be very useful to accelerate the equilibration of the supramolecular fiber in solution. Moreover, we demonstrate that combining the two methods in opportune way allows to take advantage of the strong points of both, providing an equilibrated configuration for the BTA supramolecular polymer in a faster and more reproducible way compared to classical simulations. The versatility of this approach suggests that the latter can be adapted to simulate a variety of supramolecular polymers as well as different types of supramolecular assemblies.

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Davide Bochicchio, Giovanni M. Pavan. 2018-03-28. Accelerated Atomistic Simulations of a Supramolecular Polymer in Water. https://arxiv.org/abs/1803.10491

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