Anyone interested in learning how to use the new CCP-BioSim BioSimSpace Python environment for easy setup, running, management and analysis of advanced biomolecular simulations.
Knowledge of Python, e.g. as gained from the Python for Biomolecular Modellers workshop.
Knowledge of BioSimSpace, e.g. as gained from the Introduction to BioSimSpace workshop.
Alchemical free energy calculations can be used to efficiently compute binding free energies between a ligand and a protein or hydration free energies of a small molecule. In the last few years, the use of such methods has gained momentum not only within academia but also within the pharmaceutical industry. In order to run alchemical free energy simulations, a series of molecular dynamics simulations need to be carried out. In the first part of this workshop you will learn how to set up, run, and analyse, binding free energy calculations with BioSimSpace.
Metadynamics is an advanced simulation method that can be used to bypass large free energy barriers allowing the estimation of free energies for processes that would normally be impossible to observe. The method relies on the concept of "collective variables", which are used to describe the pathways between basins on the free energy surface, e.g. the distance between the centre of mass of a ligand and the binding site in a protein. In the second part of this workshop you will lean how to use BioSimSpace to set up metadynamics simulations for simple collective variables that can be run using GROMACS and PLUMED.
The workshop consists of a series of Jupyter notebooks. To run these, you will first need to create a BioSimSpace conda environment:
conda create -n openbiosim -c conda-forge -c openbiosim biosimspace=2023.1.0
conda activate openbiosim
These training materials will teach you more about BioSimSpace, including how to write your own BioSimSpace code. The material is split into two parts.
- alchemical_setup.ipynb : This notebook shows you how to use BioSimSpace to set up alchemical free energy simulations that can be run with SOMD or GROMACS.
- metadynamics.ipynb : This notebook shows you how to use BioSimSpace to setup, run, and analyse metadynamics simulations using GROMACS and PLUMED.