This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
Though Python is a very popular and powerful environment for Biomolecular Simulation, many important and well-established tools require working from the command line in a terminal window. So it's an advantage to be familiar and comfortable with both ways of working.
This workshop demonstrates two approaches to running MD simulations on a simple protein system:
- From the command line in a terminal window, using AMBER
- In Python, via a Jupter Notebook, using OpenMM
The focus is on the preliminary simulations that are required to relax and equiliobrate an initially-built system, so that later "production" simulations have the best chance of being stable and reliable.
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/protein-simulation-workshop:latest
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/protein-simulation-workshop:latest
Workshop Content Authors:
- Charlie Laughton
Please direct all questions and feedback to Charlie Laughton