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Welcome

Welcome to to the Wiki for the "Setting Up Simulations" section of the CECAM Extended Software Development Workshop, Juelich 12-25/10/15.

Overview

Objective: The aim of this sub-workshop was to introduce participants to alternative paradigms and toolkits for setting up molecular dynamics simulations, including validating starting structures and repairing "errors", embedding solutes in solvents and membranes, relaxation and equilibration protocols, and setting up complex simulations such as free energy perturbation calculations. Participants had the opportunity to explore the capabilities of a range of web-based (e.g. http://mmb.irbbarcelona.org/MDWeb/) and python toolkit-based solutions (e.g. http://www.hecbiosim.ac.uk/fesetup), and in a "hackathon" type activity, worked in small groups with the code owners to tackle problems related to unmet needs, flexibility, interoperability, or performance.

In accordance with tradition, the Hackathon was fuelled with pizza...

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Theme leaders

Modesto Orozco & Adam Hospital (University of Barcelona)

Adam has been one of the key developers of the Web-based MD support tools produced by the Orozco Group at the University of Barcelona, such as MDWeb. Details of the software requirements and material on the tutorials can be found here

Hannes Loeffler (Daresbury Laboratories)

Hannes is the lead developer of FESetup, a Python toolkit for the automated and high-throughput preparation of Free Energy Perturbation calculations of ligand-protein binding energies. Details of the software requirements and material on the tutorials can be found here

Phill Stansfeld (Oxford)

Phill is lead developer of the infrastructure behind MemProtMD - a database of Membrane Protein MD simulations. Details of the Software requirements can be found here

Timetable

16th October:

  • 9-9:15 registration
  • 9:15-9:20 Opening remarks (Charlie Laughton)
  • 9:20-10:10: Modesto Orozco
  • 10:10-10:30: Coffee
  • 10:30-11:15: Hannes Loeffler
  • 11:15-12:00: Phill Stansfeld
  • 12:00-12:45: Lunch
  • 12:45-14:45: Parallel tutorial workshops 1
  • 14:45-15:00: Coffee
  • 15:00-17:00: Parallel tutorial workshops 2
  • 17:00-17:30: Hackathon group formation

17th October:

  • Morning: Hackathon
  • 12:00-14:00: Lunch at pizzeria (bus transport)
  • 14:00-16:00: Hackathon part 2.
  • 16:00-16:45: Group presentations and prizes.
Congratulations to the winning team: Emiliano Ippoliti, Prajwal Nandekar, and Khaled Tumbi!
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Course shared Googledoc:

https://docs.google.com/document/d/1mAQR_dNE1V_tXoFpGMKzSUL87JRdDtKG_uxSsOwMq3E/edit?usp=sharing

Updated