Welcome to our tutorials and training. Each tutorial listed below is designed to be a self contained learning experience. We endeavour to provide tutorials that are free from bugs/glitches and errors, to this end we test and verify to the best of our ability. However it is inevitable that some problems escape unnoticed, should you encounter a problem, regardless of how trivial please report it to either the author of the tutorial or to This email address is being protected from spambots. You need JavaScript enabled to view it..


Simulation Analysis with MDTraj

icon mdtrajAn online training course designed to provide a basic introduction to the use of Jupyter notebooks for the interactive analysis of molecular dynamics simulation data. The course will introduce the popular libraries numpy, matplotlib and MDTraj and is suitable for beginners to molecular dynamics and those new to these tools.

The training course can be found here

Molecular Visualisation, Modelling and Dynamics

icon md setupAn online training course consisting of three parts aimed at beginners to biomolecular simulation. The training course parts consist of:

1. Getting to grips with biomolecular visualisation.

2. Setting up simple molecular dynamics simulations with NAMD.

3. How to setup a simple protein-ligand simulation.

The training course can be found here

Automating Simulation Submission to HPC

icon longbowLongbow is a tool developed by HECBioSim under a collaboration between STFC and Nottingham University. The main goal of Longbow is to allow users to seamlessly offload one/masses of simulations to a HPC resource in a manner that is no different from if they had run them on their PC.

This training exercise is aimed at beginner users to high performance computing, those new to Longbow or those from non-traditional backgrounds such as experimentalists.

The training course can be found here

The Analysis of MD Simulation Data

icon md analysisThis training course is designed to give a basic introduction to methods for the evaluation of sampling and convergence in molecular dynamics simulations. In particular the focus of this course is a comparison of methods based on RMSD analysis and those based on PCA. This training course is suitable for beginners and relatively new users to molecular dynamics.

The training course can be found here