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