Afternoons, weeks 2-4, are set aside for practical excercises covering the use of molecular dynamics (MD) to simulate biomolecules. The excercises take place in two parts.

The first covers the use of VMD for visualising molecules and the results of an MD simulation. For this you will need to download the VMD code, a VMD tutorial and a set of work files used in the tutorial. This is an enabling tutorial as you will use VMD to run NAMD. The most important parts of this tutorial are chapters 1 and 3; chapter 6 may also be useful, while chapters 2 and 4 are very quick to work though.

The second excercise covers the use of NAMD (a general purpose MD package designed to work on both single stand-alone computers and parallel clusters). for this you will need the NAMD code, a NAMD tutorial (available in Windows and Mac/Linux forms) and a set of files used in the tutorial.

Problems with VMD on your Mac?

Have a look at the following FAQ answers to see if they help

• Using VMD in text mode: option 1?
• Using VMD in text mode: option 2?
  

Assessment

The assessment for the workshops is described at this link.

 Additional notes for the NAMD tutorial when using this under Windows:

(1) More recent versions of this tutorial get you to run commands by typing

               "source ..."

in the TkCon window. An alternative is to type

               "vmd -dispdev text -e ..." in a terminal window.

Note that if you find older versions of this tutorial, they will use the latter approach, but change the command to typing "vmdtext -e ...." in a terminal window, but the "vmd -dipsdev text" form is the correct, general, form of this command.

(2) The VMD command window mimics a linux environment, and as such it does not like spaces in file/directory names. This has two consequences.

1. When you type a directory name in the command window you should use the forward slash (/) to separate directories instead of the back-slash (\) used in DOS-based systems like Windows
2. Where you have spaces in the names (e.g. c:\My Documents) you will need to "escape" them by putting a "\" in front of the spaces. for example, "C:\My Documents" should be enterred as "c:/My\ Documents" 

(3) The workshop refers to common unix utilities like "nedit" for text editing and "xmgrace" for graphing data. These can be replaced by "notepad" and "Excel", respectively (or any editor & data-processing program you wish to use).