Modeling Synthetic Ion Channels with Coarse-Grained Molecular Dynamics

This tutorial recreates the study, "Synthetic Ion Channels via Self-Assembly: a Route for Embedding Porous Polyoxometalate Nanocapsules in Lipid Bilayer Membranes" [Rogan Carr, Ira A. Weinstock, Asipu Sivaprasadarao, Achim Müller, and Aleksei Aksimentiev. Nano Lett., 8:3916-3921, 2008.], to demonstrate how one designs and implements a research project using molecular dynamics (MD) as a tool. The researcher will learn to create and visualize systems in Visual Molecular Dynamics (VMD) using the TCL interface, create coarse-grain models of biological and metallic molecules and perform MD simulations with NAMD. Requires VMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.

Example applications