BioExcel CoE Newsletter #3

Dear reader,

You are receiving this mail either because you subscribed for the BioExcel's newsletter through the website or you attended one of our webinar events. Since we are organizing regularly more of the latter, we thought you'd like to know about them. You can, of course, always unsubscribe (link is at the bottom) but we hope you'd like to stay in touch with us.

Rossen Apostolov
BioExcel Project Manager


Interest Groups (IGs)

Expertise and services in BioExcel cover a broad part of the computational biomolecular research domains. Scientists, however, typically focus on a specific sub-domain and apply selected methods and software in their investigations. In order to provide targeted support in some areas of high interest, we have launched several interest groups to enable researchers to improve and accelerate their work through closer interactions with experts. The initial interest groups are:

• Biomolecular Simulations for Entry Level Users IG

• Integrative Modelling IG

• Free Energy Calculations IG

• Hybrid Methods for Biomolecular Systems IG

• Best Practices for Performance Tuning and Optimization IG

• Practical Applications for Industry IG

Given the interest in the community, we could organize additional groups. You can read more about the groups and join them on our dedicated IG page.


Webinar on Free Energy

Free energy (FE) is part of the energy of a given system that can be converted into valuable work. Although very useful, making accurate calculation of the FE can be quite challenging. Yet, if done right (and fast, and easy!) the benefits are great (check that with your friend, the staff scientist at BigPharma Inc.). Prof. Bert de Groot is presenting our next webinar to show one such approach for automated FE calculations using the tool pmx (which, of course, has GROMACS on the back-end :))  As always there will be a Q&A session at the end to put your questions to Bert!

Webinar #4: Mutation free energy calculations with pmx

Webinar #4: Mutation free energy calculations with pmx

Join us on Friday 10th June for the fourth webinar in BioExcel’s webinar series on  computational methods and applications for biomolecular research. The series cover broad topics related to the latest development of major software packages; their application to modelling and simulation; best practices for performance tuning and efficient usage on HPC and novel architectures; introductory tutorials for novel users and much more. …

Read more.

Coming up next

On Jun 30th we will have a webinar on QM/MM approaches for biomolecular modellig and simulations. Check our website for more details and registration soon!


SIG BioExcel: 1st Annual Meeting during ECCB2016 in Hague

This is the main venue to meet the BioExcel team, learn about the cutting-edge advances of our work and meet other computational scientists from academia and industry; software developers; commercial vendors and resource providers. Registering for the event will let you:

• Showcase your success story (send an abstract for a poster presentation and selected flash talk in front of top scientists in the field!)

• Discuss upcoming challenges

• Share experience and best practices

• Get an opportunity for networking and collaboration projects

• Provide input for the development of our software and workflows

Check out the program and hurry-up with the submission!

SIG BioExcel 1st Annual Meeting: "Advanced Simulations for Biomolecular Research”

SIG BioExcel 1st Annual Meeting: "Advanced Simulations for Biomolecular Research”

SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. It brings together stakeholders of 1) core applications that are supported by the center - HADDOCK (integrative modelling), GROMACS (molecular dynamics simulations) and CPMD (hybrid QM/MM methods) and 2) worklow environments and platforms for data integration and analysis such as Galaxy, Taverna, Open …

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The latest beta of GROMACS is out to give it a try! (we have moved to a new naming scheme for the versions, thus there will be no GROMACS 6)

New Release: GROMACS 2016-beta2

New Release: GROMACS 2016-beta2

The second beta release of GROMACS 2016 is available! We are making this available to you to get an early taste of how GROMACS 2016 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of GROMACS as high as possible, we’re only human and can get things wrong, and we need …

Read more.


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Video channel - here are the recordings of the webinars!