The CCPBioSim training week saw another jam packed schedule of short training courses aimed at researchers interested in biomolecular simulation. The event was well attended with between 30 and 40 delegates attending each day, attendees were from a wide variety of research backgrounds from those that have no biosimulation experience at all through to those that have mastered some techniques and were looking to expand their skill set into other areas or new tools. 


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Photographs taken from the workshop event.


The first day saw users that are of beginner or non-traditional to biomolecular simulation get to grips with a new software plugin for PyMOL called enlighten. It shown how simple it can be for users not familiar with Linux or standard tools to setup protein-ligand simulations that can give them a much better insight into their problems than static structures might give.

Day two started with a more general introduction to molecular dynamics using NAMD, and some common tools which biosimulation researchers commonly use such as VMD. Before moving onto a workshop on Longbow, the remote job submission and management utility developed by HECBioSim, this workshop focused on removing the complexities on writing job submission scripts and introduced delegates to high volume simulation. Finally the last workshop on day two focused on a tool for analysing high volumes of MD data PyPCAZIP, users were introduced to the principles and basic functionality of the tool and how it can be used to inform better research practice and quality of data.

On day three, delegates started out by learning about the Python scripting language and how it can be applied to biomolecular simulation. This workshop was aimed at delegates of all ability ranges from beginner through to seasoned Python coders. The second part of this workshop day was dedicated to FESetup, a tool developed by CCPBioSim for the automated setup of free energy simulations and more. Delegates were introduced to the basic functionality of FESetup and worked on some tutorials to explore more advanced functionality of the automation software.

Day four of the training week was dedicated to Monte Carlo methods for biomodelling. Delegates started out learning about the basic principles of Monte Carlo simulation, how it works and how to implement a Monte Carlo program. They then went on to learn about how to put all that together to simulate biomolecular problems, before going on to running some real simulations to calculate protein-ligand binding energies.

The final day of the training week was dedicated to Quantum Mechanics/Molecular Mechanics (QM/MM), which introduced the non-specialist to the methods applied to enzyme-catalysed reaction mechanisms using CHARMM.

The workshop received positive overall feedback from delegates, with a selection of their comments below:


“As a PhD student without a background in computer science I found the courses/workshop interesting and an insight into the potential ways to approach problems in the future. I will definitely learn python!” - Attended Wednesday to Friday


“It has been a very informative workshop. Thank you for organising it. Cheers!” - Attended Wednesday


“Excellent workshop! Followable and instructive.” - Attended Tuesday


“Very useful, MC can definitely be applied to some of my work. Good material.” - Attended Thursday


“Excellent set of workshops. Each one useful in its own right and also fitted together well. Would be good to use the output of FESetup in a simulation and add that to the training.” - Attended all days


“Simply amazing! :-)” - Attended Wednesday