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:
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
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
If you have any questions or comments on this tutorial, please email the TCB Tutorial mailing list at firstname.lastname@example.org. 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/.
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.
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 Programs VMD menu item in Windows.