Introduction

This tutorial is designed to guide users of VMD and NAMD in all the steps required to set up a molecular dynamics (MD) simulation of a bionanotechnology device. The tutorial assumes that you already have a working knowledge of VMD and NAMD. For the accompanying VMD and NAMD tutorials go to:
http://www.ks.uiuc.edu/Training/Tutorials/
This tutorial has been designed specifically for VMD 1.8.5, and should take about 4 hours to complete in its entirety.

Structure building for biomolecules is likely familiar to most VMD and NAMD users and the interested reader is referred to the in-depth treatment given in the other VMD and NAMD tutorials. Constructing models of solid-state inorganic systems, however, requires a slightly different approach. Therefore, we begin in the first unit by learning how to build models of synthetic devices, starting with only a crystal unit cell. We'll then add solution and end by simulating ionic current through a nanoscale pore in a crystalline membrane. The second unit will guide you through combining a biomolecule (DNA) with a crystalline membrane and simulating the resulting system. Many of the steps in this tutorial depend on the results of previous steps. If some steps are not completed and you would like to move on, exemplary output is available in bionano-tutorial-files/example-output/.

Throughout the text, some material will be presented in separate ``boxes". These boxes include information complementary to the tutorial, such as details of the systems used in bionanotechnology research, tips or technical details, and suggestions for more in-depth simulations.

If you have any questions or comments on this tutorial, please email the TCB Tutorial mailing list at tutorial-l@ks.uiuc.edu. The mailing list is archived at http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/tutorial-l/ http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/tutorial-l/.

Required programs

The following programs are required for this tutorial:

• VMD: Available at http://www.ks.uiuc.edu/Research/vmd/ http://www.ks.uiuc.edu/Research/vmd/ (for all platforms)

• NAMD: Available at http://www.ks.uiuc.edu/Research/namd/ http://www.ks.uiuc.edu/Research/namd/ (for all platforms)

Getting Started

You can find the files for this tutorial in the bionano-tutorial-files directory. Below you can see in Fig. 1 the directory structure for this tutorial.

Figure 1: Directory structure of bionano-tutorial-files.

To start VMD type vmd in a Unix terminal window, double-click on the VMD application icon likely located in the Applications folder in Mac OS X, or click on the Start $\rightarrow$ Programs $\rightarrow$ VMD menu item in Windows.

Acknowledgments

Development of this tutorial was supported by the National Institutes of Health (P41-RR005969 - Resource for Macromolecular Modeling and Bioinformatics).