Tutorial: Tools for Advanced Sampling of Macromolecular Systems

Welcome to the tutorial wiki pages. Everything you will need for the tutorial can be found from this page.

Any questions, please ask or email ibethune@epcc.ed.ac.uk

Local arrangements

This info is all on the web page where you registered for the tutorial.

Programme

Follow the links below in the programme to find the slides from each talk, and instructions for the hands-on sessions:

Day 1

• 9.00 - Registration
• 9.30 - Introduction (Iain Bethune)
• 10.00 - Overview of Computing Environment (Iain Bethune)
• • Setup Instructions
• 10.30 - Coffee Break
• 10.45 - Analysing MD data with CoCo (Charlie Laughton)
• 12.15 - Lunch
• 13.15 - Non-linear dimensionality reduction with LSDMap (Eugen Hruska)
• • Analysing MD data with LSDMap
• 14.45 - Coffee Break
• 15.00 - ExTASY Advanced Sampling Workflows
• • Introduction to the CoCo-MD workflow (Charlie Laughton)
• • Introduction to DM-d-MD (Eugen Hruska)
• • Running Sampling Workflows using ExTASY (Iain Bethune)
• • Hands-on Instructions
• 17.00 - Finish

Day 2

• 9.30 - Introduction & Recap (Iain Bethune)
• 9.45 - Introduction to Ensemble Toolkit and RADICAL-Pilot (Shantenu Jha & Andre Merzky)
• • Exercises
• 11.15 - Coffee Break
• 11.30 - The "Ex" in ExTASY: Extending ExTASY Workflows using Ensemble toolkit (Shantenu Jha & Andre Merzky)
• 12.15 - Lunch
• 13.15 - Automated dataflow algorithms for advanced ensemble molecular dynamics sampling (Erik Lindahl, BioExcel)
• 14.15 - Overview of afternoon tracks (Iain Bethune)
• 14.30 - Coffee Break
• 14.45 - Hands-on sessions:
• • Applications Option: Applying workflows to example problems (Charlie Laughton & Eugen Hruska)
• • Software Development Option: Installing ExTASY on your own computer and cluster, Implementing new workflows (Shantenu Jha & Andre Merzky)
• 17.00 - Finish

Feedback Form

At the end of the tutorial, please complete the online feedback form. It should take only a few minutes and is very helpful to us!