Past Events

CCPBioSim Training Week - Day 2: Running and analysing MD simulations
Tuesday 07 June 2016

Workshop Material

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

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:

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:

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

12.00 pm - 12.30 pm  Longbow part 1 (introduction)

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:

Marc van der Kamp: This email address is being protected from spambots. You need JavaScript enabled to view it.