Issue 53 | February 2024
Dear reader,

Find out more about recent developments to our four key software tools. These developments were influenced by the feedback which our users provided through the surveys we ran during 2023. It's a final call to register for some key BioExcel training events, including the Summer School on Biomolecular Simulations 2024 - don't delay! If you don't want to wait util the summer for some training on molecular simulation, there are still places available on the Comp Chem Spring School 2024 being held in April. We continue with our webinar series and next up is what's new in GROMACS 2024. Continue reading for all this and more in this edition of the BioExcel newsletter.

The BioExcel Team

BioExcel core software updates

In line with our aim to be more user-driven in the development of our software, workflows and training material, we provide a short update on some of the recent work carried out on each of our four key applications. This work is based on the priorities which emerged from our 2023 user surveys and is reflected in our software development dashboard.
GROMACS: earlier this month saw the release of GROMACS 2024 which comes with new features such as an interface to COLVARS, an improved deform option as well as some improvements to the Accelerated Weight Histogram (AWH) implementation. This is the topic of our upcoming webinar on 5 March so if you have not registered you still have time.
HADDOCK: the development team has consolidated the HADDOCK3 (beta release) code, adding the following new modules and continues to work toward the first production release for which extensive documentation needs to be written.
  • OpenMM module allowing the refinement of complexes using molecular dynamics simulations.
  • Alanine scanning module to perform systematic scanning of residues at the interface between two molecules to identify residues which contribute most to the interaction.
  • Contactmap module for the generation of interactive contact heatmaps and chord charts, facilitating the visualisation of the interactions in a complex.
PMX: a new tutorial on 'Estimation of Solvation Free Energy' using GROMACS+PMX (non-equilibrium TI) is available.
BioBB: a new module wrapping some functionalities from the pdb-tools (a dependency-free, cross-platform swiss army knife for PDB files) library developed in the Bonvin lab is available: GitHub, Conda Package, Read the docs.

BioExcel Summer School 2024: final call

This is the final call for our Summer School on Biomolecular Simulations which will take place in Sardinia in June. This will be the 8th edition of this popular event aimed at PhD and post-doctoral researchers using or planning to use biomolecular modeling and simulation in their everyday research. The Summer School features a combination of lectures and practical sessions delivered by the main software developers. Follow the link for more information and how to register. Deadline is Friday 8 March 2024.

CSS / BioExcel Comp Chem Spring School

If you are interested in a comprehensive, tutorial-style, hands-on, introductory and intermediate-level treatment of the essential methods for molecular modelling and computational chemistry using modern supercomputers then the Computational Chemistry Spring School 2024 is for you. The deadline for registration is fast approaching: 17 March 2024.

Webinar series

On 5 March 2024 Magnus Lundborg, who leads the GROMACS development team at KTH in Sweden, will talk about the new features and improvements in GROMACS 2024 including an interface to COLVARS, an improved deform option as well as some improvements to the Accelerated Weight Histogram (AWH) implementation. Register for this webinar here. Following this, our 19 March 2024 webinar will be dedicated to COLVARS. More information will follow on our social media channels and our website.

BioExcel conference: book the date!

On 20 - 23 October 2024 we will be holding our 2nd BioExcel Conference on Advances in Biomolecular Simulations. The conference will take place in Brno, Czech Republic and will have a similar flavour to our first BioExcel Conference on Advances and Challenges in Biomolecular Simulations which took place in 2021. We have a number of top speakers lined up and we will be adding a few more once these are confirmed. Registration will open next week so keep checking our social media channels and the official event webpage. Don't miss out!

Alchemical Free Energy workshop: final call

Last call for the Alchemical Free Energy workshop which is being held 13 - 15 May in Leiden, The Netherlands. The event will gather experts from industry and academia to discuss use cases, pitfalls and their solutions; as well as challenges and possible paths forward to improve the practical application of free energy calculations in drug design. Don't miss out!

GROMACS on LUMI workshop blog

Read the blog by Xavier Anthony Raj from CSC in Finland on the recent workshop on 'How to run GROMACS efficiently on the LUMI supercomputer'. As well as some of the key highlights and learning points you will find a link to the materials used during the workshop.

BioExcel-CV19 featured in CORDIS

We are delighted that our work to develop the BioExcel-CV19 database of Molecular Dynamics trajectories has been featured on the European Commission's Community Research and Development Information Service (CORDIS).

BioExcel is a featured community on Zenodo

Our ongoing efforts to share our materials for the benefit of the community through the Zenodo repository have been highlighted. Check out what the BioExcel community on Zenodo has to offer.

Request: please acknowledge BioExcel support

We are passionate about providing high quality support to users of our codes and have done so for many years. We have a small favour to ask those who have received this support and read this message.
Please take a moment to acknowledge the BioExcel Centre of Excellence as part of your dissemination through journals, presentations or other forms of communication. It would mean the world to us! Further, we would be delighted if you could drop us a quick email at to let us know how we have helped you. Thank you for your continued support!
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