Overview

The afternoon sessions (2-4pm) are set aside for practical excercises covering the use of molecular dynamics (MD) to simulate biomolecules. The excercises take place in three parts:

1. Practical computer skills for molecular simulation [Week 1].
   
2. Use of Visual Molecular Dynamics (VMD) for visualising molecules and the results of an MD simulation [Week 2].
   
3. Use of NAMD (a general purpose MD code) for simulating biomolecules [Weeks 2-4].

Things to do before the workshop

The workshops require use of the Centre for Scientific Computing (CSC) Linux computers. You will access the CSC computers remotely from your laptop using the NX client. Prior to the workshops you will need to follow the instructions below to set up a CSC account and install the NX client.

Please also re-familiarise yourself with the university regulations on computer use (e.g. no sharing of computer accounts or passwords).

Set Up a CSC account

To set up a CSC account follow this link and proceed to the CSC Account Creation Page. You will need your existing ITS usercode and password to access this page. On the account creation page make sure that you choose a strong password. Unless you have a strong preference otherwise, choose the Bourne-Again SHell. For your research group membership select Other/Not Listed.

Install the NX Client

The recomended way to access the CSC computers from laptops is via the NX remote desktop. To download and install the NX client on your laptop follow these instructions. The NX client will connect you to the CSC server godzilla.

Demonstrator

The assigned demonstrator for the workshops is Daniel Pearce.

Assessment

The assessment for the workshops is described at this link.