from 29 June 2015 to 1 July 2015
This course will take place at University of Strathclyde
Europe/London timezone

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:

  • Understand the basic physics of Molecular Dynamics and use these to make appropriate choices for force fields, system sizes and timestep.
  • Set up, run and analyse the results of MD simulations on ARCHER using NAMD & DL_POLY.
  • Perform scalability tests and select an optimal number of processors for a calculation

Prerequisites

Timetable

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

Starts 29 Jun 2015 09:00
Ends 1 Jul 2015 17:30
Europe/London
This course will take place at University of Strathclyde
Royal College room 473
University of Strathclyde, Royal College room 473 https://www.strath.ac.uk/maps/royalcollegebuilding/

This course is part-funded by the PRACE project and is free to all. Please register using the online form. If you have any questions, please consult the course forum page or contact epcc-support@epcc.ed.ac.uk.