Introduction to Molecular Dynamics on ARCHER @ EPCC at University of Strathclyde

Jun 29, 2015, 9:00 AM → Jul 1, 2015, 5:30 PM Europe/London

Royal College room 473 (This course will take place at University of Strathclyde)

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

• 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.

Timetable

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

Slides http://www.training.prace-ri.eu/events/?tx_typopresscalendar_pi1[uid]=144&no_cache=1

Monday, June 29

Registration

Introduction (IB)

MD Overview: Basics of force-fields(KK-O)

Break

MD Continued: Integration, Thermostats, Barostats, Constraints (KK-O)

Lunch

Introduction to NAMD (KK-O)

Break

Practical: Running NAMD on ARCHER (IB / KK-O)

Tuesday, June 30

Advanced NAMD & VMD: PME method, setting up, visualisation, Steered MD (KK-O)

Parallelisation & scaling of NAMD (IB)

Break

Practical: Further NAMD on ARCHER (IB / KK-O)

Lunch

DL_POLY: Introduction & Overview (IT)

Break

More DL_POLY: Rigid Bodies? (IT)

Wednesday, July 1

Practical: DL_POLY on ARCHER (IB / IT)

Ab-initio MD (IB)

Break

Practical: More DL_POLY on ARCHER (IB / IT)

Lunch

Practical: Extension exercises for NAMD & DL_POLY (IB / KK-O / IT)