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Basic Analysis Workshop

In this workshop we will explore some of the issues in simulation preparation and analysis that can trip up the unwary, and how to avoid them

Basic Statistics Workshop

This workshop illustrates how basic statistical concepts can be applied to the analysis of biomolecular simlation data

Clustering Workshop

This tutorial/workshop illustrates the application of a variety of clustering methods to an MD trajectory, comparing their performance

Equilibration Workshop

This workshop 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.

PCA Workshop

The aim of this workshop is to illustrate methods we can use to assess convergence and sampling in MD trajectories

PDB2PQR Workshop

This short workshop 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!

Lysozyme MD simulation with aiida-gromacs

Data provenance with Justin Lemkul's lysozyme in water simulation

GPCR coarse-grained simulation setup with aiida-gromacs

Advanced data provenance with coarse-grained setup of an embedded GPCR

Introduction to Python Programming

This workshop will introduce more intermediate features of Python that are useful for biomolecular modellers.

Introduction to Structure Validation

This workshop will introduce methods to deduce that starting structures for preparing simulations represent high quality starting points.

QM/MM Workshop

The training workshop will introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms.

Ubiquitin Analysis Workshop

This workshop 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?