Training
We provide access to training courses that have been previously run as instructor led workshops. These courses are made available for everyone to learn about topics from the simple to the more advanced. We have categorised these below, please report any problems using our contact form.
An Introduction to Python Programming
This course will introduce more intermediate features of Python that are useful for biomolecular modellers.
An Introduction to Structure Validation
This course will introduce methods to deduce that starting structures for preparing simulations represent high quality starting points.
aiida-gromacs - Lysozyme MD simulation tutorial
Data provenance tools demonstrated with Justin Lemkul's lysozyme in water simulation tutorial.
An Introduction to Equilibration
This course looks at one of the most common methods for assessing equilibration: the calculation of RMSDs. It may be a common approach, but is it a good one? Maybe not.
An Introduction to PDB2PQR
This short course illustrates the application of pdb2pqr to the analysis of the tautomeric and ionization states of residues in the structure of the cysteine protease cruzein (PDB code 2oz2) - the results may not be what you would have expected!
Preparing Proteins for Simulation
This course walks through the process of preparing a simple protein system for molecular dynamics simulation using Ambertools.
Running DNA Simulations
This course introduces tools for running simulations on DNA systems.
Running MD Simulations
This workshop demonstrates two approaches to running MD simulations on a simple protein system.
Introducing Basic Statistics
This course illustrates how basic statistical concepts can be applied to the analysis of biomolecular simlation data
Introducing Basic Analysis
In this course we will explore some of the issues in simulation preparation and analysis that can trip up the unwary, and how to avoid them.
Introduction to Analysis of Ubiquitin
This course illustrates the application of a number of Python-based tools to the analysis of the results from a short (1 nanosecond) simulation of ubiquitin, investigating the question, how similar is the MD trajectory to the crystal and NMR structures?
An Introduction to Clustering
This course illustrates the application of a variety of clustering methods to an MD trajectory, comparing their performance.
An Introduction to Principle Component Analysis
The aim of this course is to illustrate methods we can use to assess convergence and sampling in MD trajectories.
Analysing with MM-GBSA
This course walks through the process of perfprming a basic MM-GBSA analysis of a molecular dynamics simulation of a protein-ligand complex to estimate the ligand binding free energy.
Protein Analysis with Machine Learning
This course introduces the application of Machine Learning methods (specifically, PCA and clustering) to the analysis of protein simulation data.
Introduction to the Analysis of Proteins
This course introduces the application of MDTraj to the analysis of protein simulation data.
aiida-gromacs - GPCR MD simulation tutorial
An advanced demonstration showing advanced GPCR workflow with full data provenance collection.
Introducing Docking Workflows
This course introduces docking tools and workflows.
Introducing QM/MM
The course will introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms.
Introducing Coarse-Graining
This workshop introduces tools for setup and running coarse-grain simulations.
Introducing OpenForceField Tools
This workshop introduces the openforcefield tooling.