README.md

CCPBioSim teaching at CCP5

Event Dates: From Saturday 15th July 2018 to Tuesday 18th July 2018

Summary

CCPBioSim are happy to work with CCP5 to deliver biomolecular training workshops as part of the CCP5 Summer School.

Information

• Code of conduct
• Workshop server / how to download and use at home

You can talk with each other and the trainers using the workshop etherpad. Please keep discussion respectful and remember the code of conduct.

Feedback

We are very interested in your comments about any aspect of the CCPBioSim contribution to the CCP5 Summer School. Please use the below form to anonymously comment on any aspect of our programme, e.g. the lectures or the practicals. You are the first people to use parts of BioSimSpace, so we are particularly interested in your complaints, comments and suggestions for BioSimSpace, and you experience of using these cloud-based Jupyter notebooks for running simulations.

Send feedback :-)

Programme

Monday 16th July

• Morning : Introduction to Jupyter, followed by Introduction to BioSimSpace

Introduction to Jupyter: Connect to the workshop server and navigate to the python_and_data folder. This provides a menu of lessons in Python. You only need to look at the 01_jupyter_howto.ipynb lesson. You can look at other lessons if you have time, or if you are uncomfortable with Python.

Introduction to BioSimSpace : Continuing on the workshop server navigate to the biosimspace_workshop folder. Follow the lessons in order from 01_introduction.ipynb to 04_molecular_setup.ipynb.

• Afternoon : Setting up and Running Molecular Dynamics Simulations: Good Practice and Pitfalls

Tuesday 17th July

• All day : Visualising Binding Free Energies using Swap-Based Methods