Victorian Partnership for Advanced Computing

Molecular visualization and modelling has become an increasingly important tool in chemistry and the life sciences with dozens of free and commercial applications for the researcher to use. The aim if this course is to introduce basic molecular modelling concepts and give practical exercises in using some of modelling packages.

Guest accounts will be provided for attendees that do not have an account on a VPAC Super Computer, however, if you plan to get an account in the near future, please consider applying before the course and you will be able to use your own. Please mark on your account application forms that you will be attending this course and we will try and get your account created before hand.

Topics Covered

1. Molecular simulation

• Describing the differences of various molecular simulation methods.

2. Molecular visualization - VMD/Pymol

• Basic exercises in loading structures and highlighting various structural elements.

3. Using HPC for molecular simulations.

• Brief introduction to submitting jobs to the clusters

4. Practical Excercises

• Molecular dynamics
• Namd / Gromacs tutorial files
• Ab initio simulations
• Gamess / Gaussian
• Molecular docking
• Autodock / Schrodinger maestro

This course is free to staff and students at VPAC Member Universities, however, booking in advance is essential. Please book your place by selecting a session from the list to the right of this page or for extra information, contact training@vpac.org or phone +61 3 9925 4410.