BioSimSpace tutorials

A suite of tutorials that provide an introduction to BioSimSpace, and examples of advanced functionality covering different scientific use cases. These tutorials have been tested with BioSimSpace 2023.5.0 on a linux-64 platform and require the following dependencies

• Gromacs (tested with 2023.1)
• AmberTools (tested with 23.3)
• PLUMED (tested with 2.9.0)
• cinnabar (tested with 0.3.0)
• alchemlyb (tested with 1.0.1)

Installation instructions

Option 1) Local installation using conda

This route can be used to install the tutorials on a computer.

We recommend using mamba to install the dependencies.

conda create -n  bsstutorials "python<3.11"
conda install -c conda-forge mamba
mamba install -n bsstutorials -c openbiosim -c conda-forge biosimspace=2023.5.0 gromacs=2023.1 ambertools=23.3 plumed=2.9.0 cinnabar=0.3.0 pymbar=3 alchemlyb=1.0.1
mamba activate bsstutorials

Next clone the repository

git clone https://github.com/OpenBioSim/biosimspace_tutorials

Option 2) Use OpenBioSim's Jupyter Hub server

OpenBioSim provides access to a Jupyter Hub server with a preinstalled python environment to run the tutorials. Use this route to run the tutorials from a compatible web-browser. Access to the server require a GitHub account.

Go to try.openbiosim.org

And follow the instructions in the file TUTORIALS.txt.

Tutorials suite

• 01 - Introduction
• 02 - Funnel metadynamics
• 03 - Steered molecular dynamics and ensemble building
• 04 - Alchemical free energy calculations