|
1 | | -Though Python is a very popular and powerful environment for Biomolecular Simulation, |
2 | | -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. |
| 1 | +# CCPBioSim Protein Simulation Workshop |
| 2 | + |
| 3 | +[](https://github.com/ccpbiosim/protein-simulation-workshop/actions/workflows/build.yaml) |
| 4 | +[](https://github.com/ccpbiosim/protein-simulation-workshop/pkgs/container/protein-simulation-workshop) |
| 5 | +[](https://github.com/CCPBioSim/protein-simulation-workshop/issues) |
| 6 | +[](https://github.com/CCPBioSim/protein-simulation-workshop/pulls) |
| 7 | + |
| 8 | +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. |
| 9 | + |
| 10 | +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. |
3 | 11 |
|
4 | 12 | This workshop demonstrates two approaches to running MD simulations on a simple protein system: |
5 | 13 |
|
6 | 14 | 1. From the command line in a terminal window, using AMBER |
7 | 15 | 2. In Python, via a Jupter Notebook, using OpenMM |
8 | 16 |
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9 | 17 | 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. |
| 18 | + |
| 19 | + |
| 20 | +## How to Use |
| 21 | + |
| 22 | +This training course is deployed on the [CCPBioSim](www.ccpbiosim.ac.uk) website via our cloud infrastructure, however you can deploy on your own machine with docker. |
| 23 | + |
| 24 | +Pull the container from our repository:: |
| 25 | + |
| 26 | + docker pull ghcr.io/ccpbiosim/protein-simulation-workshop:latest |
| 27 | + |
| 28 | +In our containers we are using the JupyterHub default port 8888, so you should |
| 29 | +forward this port when deploying locally:: |
| 30 | + |
| 31 | + docker run -p 8888:8888 ghcr.io/ccpbiosim/protein-simulation-workshop:latest |
| 32 | + |
| 33 | +## Authors |
| 34 | + |
| 35 | +Workshop Content Authors: |
| 36 | + |
| 37 | +- Charlie Laughton |
| 38 | + |
| 39 | +## Contact |
| 40 | + |
| 41 | +Please direct all questions and feedback to [Charlie Laughton](mailto:charles.laughton@nottingham.ac.uk) |
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