Introduction to Molecular Dynamics Showcase

By Chen-Yu Li1, Karl Steven Decker (editor)1, Aleksei Aksimentiev1

1. Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign



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In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file – and move on to more complicated examples. We will also cover how to add a description, change perspective, and frame-related comments. 


1] Kerstin Gopfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F Keyser. Ion channels made from a single membrane-spanning DNA duplex. Nano Lett., 16(7):4665–4669, 2016.
[2] Kerstin G ̈pfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F Keyser. Large-conductance transmembrane porin made from DNA origami. ACS Nano, 10(9):8207–8214, 2016.

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Researchers should cite this work as follows:

  • Chen-Yu Li, Karl Steven Decker, Aleksei Aksimentiev (2017), "Introduction to Molecular Dynamics Showcase,"

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