Event Date/s: Tuesday 07 June 2016
The material from this workshop can be accessed using the following links:
Section 1 - Set-up and running MD with NAMD material
Section 2 - Longbow for running MD on remote clusters material
Section 3 - Analysis of MD simulations material
2.11 Merchant Venturers Building, Department of Electrical and Electronic Engineering, Woodland Road, Bristol BS8 1UB.
Travel directions are at http://www.bristol.ac.uk/maps/directions/
Please note: Research talks will take place in Lecture Theatre 3 in the School of Chemistry, Cantocks Close, BS8 1TS.
There is no fee for registering for this workshop. However, participants are responsible for arranging and the costs of their own travel and accommodation. We have provided a list of recommended places to stay below, should you need overnight accommodation. To register for this workshop day only please follow this link. Delegates wishing to attend multiple workshop days during this training week must register for those days separately.
Please note: that is this is the first time that you have used the STFC event registration system then you will need to create an account before you can register for any of the courses.
10.00 - 4.00pm Tutorial workshop on Running and analysing MD simulations
4.30pm - 5.30pm Research talk (School of Chemistry, LT3)
Prof Charles Laughton - "Going Large: Harnessing the Power of HPC Resources for Biomolecular Simulation"
Computers have stopped getting faster and faster – nowadays they just get bigger and bigger. Rather than seeing this as a problem for the future of computational chemistry and biomolecular simulation, we can take advantage of it. I will describe our work developing and applying new methods to a) make it easier for computational scientists to access large-scale resources and b) make it easier for them to make sense of the deluge of data that can result; both with the aim of improving the range and quality of the computational experiments we can do.
5.30pm - 6.30pm Drinks reception (School of Chemistry, Foyer outside LT3)
Aimed at: PhD students or Postdocs that are interested in starting to use molecular dynamics simulations of biomolecules for their research.
Requirements: Basic knowledge of the Linux command line.
The programme consists of three sections:
Section 1. Set-up and running MD with NAMD
This section will be based on the tutorial material available here: http://chryswoods.com/dynamics/index.html
We will be using the highly scalable, free and open source software NAMD.
Instructors: Dr Marc van der Kamp / Dr Christopher Woods
Section 2. Longbow for running MD on remote clusters
Longbow is a tool to help with running MD simulations on HPC clusters such as ARCHER. For more information, see: http://www.hecbiosim.ac.uk/longbow
Here, Longbow will be introduced and its use demonstrated.
Instructor: Dr James Gebbie
Section 3. Analysis of MD simulations
An important part of using MD for research is to analyse and interpret the data generated. In this section, some generally applicable analyses will be introduced.
Instructor: Prof Charles Laughton
10.00 am - 10.30 am Registration and tea/coffee (in the Atrium, MVB)
10.30 am - 11.15 am MD tutorial: Molecular Dynamics
11.15 am - 12.00 am MD tutorial: Mutation Studies
12.30 pm - 1.20 pm Lunch
1.20 pm - 2.00 pm Longbow part 2
2.00 pm - 3.50 pm MD analysis (pyPcazip)
3.50 pm - 4.20pm Coffee/Tea (in the Atrium, MVB)
Accommodation is NOT included with your registration for this event. Should you require accommodation (e.g. when attending multiple one-day events), you should make your own arrangements. We can recommend the following:
Clifton House - website - 0117 973 5407
Premier Inn, Haymarket Bristol - website - 0117 910 0600
Victoria Square Hotel - website - 0117 973 9058
Berkeley Square Hotel - website - 0117 925 4000
For general workshop queries, contact: