Molecular Dynamics and Analysis using BRIDGE

Century City Convention Centre

Century City Convention Centre


Molecular Dynamics and analysis can be complicated for novitiates and researchers from neighbouring disciplines. Building upon the Galaxy Project platform, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provides the ability to get started running molecular dynamics and analyses using curated workflows.

Target Audience: Are you keen to learn how to run a protein simulation using Molecular Dynamics?Computational chemists, biologists, protein scientists, crystallographers and anyone interested in running and analysing molecular dynamics simulations who is not familiar with the command line.

Prerequisites: Basic understanding of chemistry. A basic understanding of or keen interest in molecular dynamics.

Special requirements: Bring a laptop. Have access to the CHPC cluster. Register with BRIDGE. Install molecular viewer e.g. VMD.

    • 08:00 09:00
      Registration 1h
    • 09:00 09:15
      BRIDGE Overview: why MD and the value of this platform 15m

      why MD and the value of this platform

    • 09:15 09:30
      Logging into the platform 15m
    • 09:30 09:50
      Setup of an example protein (cellulase) with CHARMM-GUI 20m
    • 09:50 10:05
      Uploading datasets to BRIDGE 15m
    • 10:05 10:30
      Running the MD workflow (Hands on) 25m
    • 10:30 11:00
      Morning break 30m
    • 11:00 11:20
      Workflows in BRIDGE: Explanation of the steps of an MD workflow 20m
    • 11:20 11:40
      Creating your own history and workflow 20m
    • 11:40 12:00
      Analysis: Run an analysis workflow and analyse data 20m
    • 12:00 12:15
      Sharing data with collaborators 15m
    • 12:15 12:30
      Analysis: complete the workflow (Hands on) 15m
    • 12:30 13:30
      Lunch 1h
    • 13:30 13:50
      Resources and Support for Galaxy and BRIDGE 20m
    • 13:50 15:00
      Bring your own data – let’s see if this can work for you (Interactive) 1h 10m
    • 15:00 15:30
      Afternoon break 30m
    • 15:30 17:00
      Q&A and testing with your own data sets (Interactive) 1h 30m
    • 17:00 17:05
      End of Workshop 5m