This course gives an introduction to running Molecular Dynamics calculations on ARCHER using the NAMD and DL_POLY software packages.
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
- Familiarity with Linux/UNIX command-line environment is assumed.
- Basic understanding of HPC and Parallel computing concepts will be helpful - we recommend participants read the Online Introduction to ARCHER (http://www.archer.ac.uk/training/course-material/online/) and completing the ARCHER Driving Test would be advantageous.
Details are subject to change, but start, end and break times will stay the same.