Introduction to Molecular Dynamics on ARCHER

This course gives an introduction to running Molecular Dynamics calculations on ARCHER using the NAMD and DL_POLY software packages.

Details

A comprehensive introduction to MD theory is given, including force-fields, integration, and constant-temperature and constant-pressure ensembles. We will also cover more practical topics such as setting up a simulation and visualising the results, and using steered MD.

During the 3-day course there will be lots of hands-on sessions to enable participants to learn the practical aspects of running MD on ARCHER, as well as explore issues such as parallel performance and scaling.

Intended learning outcomes

On completion of this course students should be able to:

Prerequisites

The are no prerequisites for this course, although a familiarity with a Unix or Linux environment is assumed.

Timetable

Details are subject to change, but start, end and break times will stay the same.

Day 1

• 9.00 - 9.30: Registration
• 9.30 - 9.45: Introduction (IB)
• 9.45 - 11.00: MD Overview: Basics of force-fields(KK-O)
• 11.00 - 11.30: Break
• 11.30 - 13.00: MD Continued: Integration, Thermostats, Barostats, Constraints (KK-O)
• 13.00 - 14.00: Lunch
• 14.00 - 15.30: Introduction to NAMD (KK-O)
• 15.30 - 16.00: Break
• 16.00 - 17.00: Practical: Running NAMD on ARCHER (IB / KK-O)

Day 2

• 9.30 - 10.30: Advanced NAMD & VMD: PME method, setting up, visualisation, Steered MD (KK-O)
• 10.30 - 11.00: Parallelisation & scaling of NAMD (IB)
• 11.00 - 11.30: Break
• 11.30 - 13.00: Practical: Further NAMD on ARCHER (IB / KK-O)
• 13.00 - 14.00: Lunch
• 14.00 - 15.30: DL_POLY: Introduction & Overview (IT)
• 15.30 - 16.00: Break
• 16.00 - 17.00: Practical: DL_POLY on ARCHER (IB / IT)

Day 3

• 9.30 - 10.30: More DL_POLY: Rigid Bodies? (IT)
• 10.30 - 11.00: Ab-initio MD (IB)
• 11.00 - 11.30: Break
• 11.30 - 13.00: Practical: More DL_POLY on ARCHER (IB / IT)
• 13.00 - 14.00: Lunch
• 14.00 - 15.30: Practical: Extension exercises for NAMD & DL_POLY (IB / KK-O / IT)
• 15.30: Finish

Course Materials

Slides and exercise material for this course will be available here.

Location

The course will take place in University of Strathclyde - rooming details to follow.

Registration

Please use the registration page to register for ARCHER courses.

Questions?

If you have any questions please contact the ARCHER Helpdesk.