Past Events

CCPBioSim Training Week 2021
From Monday 27 September 2021
To Monday 04 October 2021

All times are in the British time zone, which for these dates is GMT+1.

This is a week long series of workshops and research talks (see below for the full list). When you register you will be able to choose which sessions you will attend. The research seminars are highlighed in blue, the workshops highlighted in red are advanced workshops suitable for people with prior knowledge of molecular dynamics simulations and software, and the workshops highlighted in green are suitable for anyone. This event is online, all the sessions will be on Zoom with the links sent to registered participants shortly after the registration deadline.


   Cost: £0

   Deadline: 22 September 2021 (will not be extended)

   Link: register here

   Maximum number of participants: 40 for workshops, 400 for research seminars

   Questions: contact This email address is being protected from spambots. You need JavaScript enabled to view it.



Tuesday 28 September

9:00 – 12:00: Non-equilibrium Molecular Dynamics

              This advanced workshop is aimed at people who are already familiar with equilibrium MD. It will cover how to set-up and analyse non-equilibrium simulations. Note this workshop will be using GROMACS.

Wednesday 29 September

9:00 – 12:00: Structure Validation

              Many MD simulations start with a structure from the Protein Data Bank (PDB). This workshop is about how you validate the structures and advice to help you pick a good starting point for simulations.

15:00 – 16:00: Research Seminar – Denise Okafor

              A chance to hear about real research applications of biomolecular simulations

Thursday 30 September

9:00 – 12:00: Chemistry/Physics for Bio Simulations

              Biomolecular simulations are at the intersection of biology, chemistry, and physics. This session will focus on chemistry and physics that is useful for biomolecular simulations that people may not have encountered in their undergraduate programmes (or have forgotten).

13:30 – 16:30: Enlighten: molecular dynamics simulations of protein-ligand systems made accessible

              This workshop is aimed at experimentalists (or newcomers to simulations) who want to try running some basic simulations on their own local desktop or laptop. Enlighten is a PyMOL plugin that provides a simple graphical interface for setting up and running simulations on enzymes with substrates bound (or other protein-ligand systems). To get the most out of this workshop, you should do the following in advance:
•    Ensure you have PyMOL 2.x installed.
•    Ensure you have Docker (Desktop) installed.
Please see the links to installation instructions for these on

Friday 1 October

9:00 – 12:00: ChemShell

              This advanced workshop is aimed at people who want to perform QM/MM calculations. ChemShell is a tool which lets you mix and match your favourite quantum and classical packages and takes care of all communication and data handling between them.

14:00 – 15:00: Research Seminar – Pietro Faccioli

              A chance to hear about real research applications of biomolecular simulations

Monday 4 October

13:30 – 16:30: Python and Software

              This session will include advice about judging the quality of software, installing software, and managing dependencies and updates.

Slides / Presentations from the 2021 Training Week

Structure Validation

Introduction to ChemShell

QM/MM for Biomolecules

ChemShell Biosimulation Workflows