Molecular Modelling and High Performance Computing with Applications

June 7th-9th, John Anderson Building, room J.A. 7.30, University of Strathclyde

This three day course will cover the basic knowledge and skills required to:

run molecular dynamics (MD) simulations using the GROMACS package
visualise the results using VMD
enable participants to run their own simulations

A more detail syllabus is availabe below.

The training will be delivered by Dr Carlos Ferrerio-Rangel (Knowledge Exchange Fellow, Chemical and process Engineering) and Dr Karina Kubiak – Ossowska (ARCHIE-WeSt support team) and is available to staff and postgraduate students from ARCHIE-WeSt partner institutions. The number of places are limited and priority will be given to users of ARCHIE-WeSt. Places for users of other facilities will be subject to availability. Students who will complete the training (by attending all 5 sessions and producing a report describing their own simulations) will obtain a certificate of attendance worth 5 credits.

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Syllabus

Day 1

Build your own MD simulations
Potentials, molecules and in silico design of molecular systems and materials
Introduction to afternoon training sessions with options available for sector-specific application exemplars and hands-on tasks

Day 2

Exploring the visualisation capabilities of VMD
Post-processing with Gromacs and VMD; illustrating your research: making movies and generating reports
Afternoon training sessions with options available for sector-specific applications and tasks

Day 3

Advanced simulation tools in Gromacs
Designing numerical experiments, analysing and interpreting results
Afternoon training sessions with choice of techniques and applications