Workshop Part 2
Dates and Times of Workshop
Monday 21st February 2pm - 4pm
Tuesday 22nd February 2pm - 4pm
Overview
Use of Visual Molecular Dynamics (VMD) for visualising molecules and the results of an MD simulation. This is an enabling tutorial as you will use VMD to run NAMD.
Exercises
First download the VMD tutorial.
To run the tutorial log into the CSC using the NX client and download the set of work files used in the tutorial.
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.
To unzip the tutorial files type
tar -xvf vmd-tutorial-files.tar.gz
Remember that in order to use VMD on the CSC machines you need to load the VMD module
module load vmd
Missing files:
colouring.tcl
ubiquitin-equilirated.coor