Hear from our 2019 BioExcel/PRACE Seasonal School travel grant beneficiaries

For each of our BioExcel training events we make a limited number of travel bursaries available. We ask the beneficiaries of the BioExcel travel grant to write a blog post for us, either about their experiences at the course, their research interests or a relevant scientific topic.

The 2019 BioExcel/PRACE Seasonal School took place in Stockholm, where participants gained a comprehensive understanding of the usage of the different codes and learnt best practices about using them on HPC systems.

Mohamed Shehata 
Acibadem University, Turkey

Being a computational chemist from an experimental background makes learning different molecular dynamics tools very challenging. I used to wonder about different MD tools other than the one I use, and I used to ask myself , “Am I the only one who is struggling to improve his HPC skills, what about the other tools?”. I was so excited when I saw the call of application for this school. Reading the details of the school, I muttered “This is literally made for me”. Having the opportunity to learn from the core developers of the main programs used in biomolecular simulations and learning the basics HPC was definitely a great experience.

Imagine that you have the chance to talk everyday to the developers of your favourite tool and have a technical discussions with them, cool is not it ?. As a NAMD/VMD user, I really enjoyed the experience of VR implementation in VMD with John Stone, the main developer of VMD. I also had very useful technical discussions with Joao Rui Vieira Ribeiro, the core developer of NAMD.

On the other hand, listening to lectures from top experts every morning during the school followed by very fruitful discussions was very awesome. They welcomed our questions and answered in the best way possible. For example,  I will never forget how Prof. Erik Lindahl spent our 15 minutes walk from KTH Royal Institute of Technology to the City Center answering my question about the polarizable force field.

In addition to the technical skills I learned during the school, I had the opportunity to meet excellent students from different countries who had similar concerns and struggle to learn like me. Our discussions together gave me the feeling that I am not alone in this learning process and everyone struggle to learn. This helped me get rid of the lack of self-confidence and increased my dedication to learn more.

The organization of the school lead by the PRACE team led by Lilit Axner was perfect. Everything was punctual, the team was very helpful, and the food was very healthy and amazing. And of course, the unforgettable boat trip between Stockholm islands.

I am also very grateful to BioExcel to give me the opportunity to attend this amazing school and support me with their travel grant to cover the cost of attendance. Beyond the idea of  money, the grant makes me feel very appreciated as a PhD student who is learning through BioExcel. You feel that there are people who want to help you to learn and grow and that you are not alone 😊

Sanja Škulj
Institut Ruđer Bošković, Croatia

The 2019 PRACE/BioExcel Seasonal School held at KTH, the Swedish Royal Institute of Technology was an exclusive opportunity to learn about recent research achievements and breakthroughs in computational biochemistry, molecular modelling and simulations. It was an honour to attend lectures, gather valuable advices and learn new and deep ideas from core developers of different program packages, namely GROMACS, NAMD, AMBER and VMD.

The school was a unique experience where I expanded my knowledge in the usage of different simulation setups with GROMACS, also learning advanced molecular visualisation and analysis tools available within VMD program package. This was also a great chance to compare performance of GROMACS package with two other codes, NAMD and AMBER, and to relate advantages and disadvantages of different codes in practice for different biochemical setups. Hands-on sessions on Beskow system at the computer laboratories of PDC Center for High Performance Computing, helped me understand how different simulation codes work on HPC systems and how to prepare setups for different types of simulations. Particularly useful for my work and PhD research, in which I focus on assisted proton transfer across mitochondrial membranes, are new ways and ideas of avoiding potential issues in biomolecular systems and their setups. Moreover, it was very insightful to see a comparison of a variety of different force fields which were developed with biological applications in mind.

During social events I had the chance to exchange ideas, to discuss with other researchers in related scientific fields and to brainstorm about our results. In this respect, witnessing different technical and scientific approaches to similar topics, where the benefits of the aforementioned codes were demonstrated, was incredibly helpful for my career development. Overall, it was a pleasure to be a part of PRACE/BioExcel Seasonal School and the knowledge I gained from people who are both experts in the field and core developers is especially motivating and beneficial for my scientific career development and valuable for my further research.

Ahmed Rozza
Budapest University of Technology and Economics, Hungary

The school provided a great opportunity that would help me in my Ph.D. research and achieve it more efficiently. Since my project focuses on MD simulations of heme proteins, and requires long calculations times which made to look for a course presents more about general usage, optimization and parallelization features for programs such as GROMACS, NAMD, and ABMER, their use on today’s HPC systems, and how to choose the optimum set of program options and inputs for a given HPC computer. The PRACE/BioExcel Seasonal School delivered a full opportunity for practice and constructive dialogue. It was an ideal platform consists of researchers, education scientists, technologists, and industry representatives who are experts in HPC, software development and biomolecular simulations

On day one, I got useful information such as the PDC-HPC environment and announcement of HPC-Europa3 project which provides access to world-class HPC systems. As mentioned on the first day of the course schedule about VMD, John Stone (Senior Research Programmer) gave us a wonderful lecture on Preparation and Analysis of Molecular and Cellular Simulations. He enlightened us with great knowledge about VMD and features upcoming in the new version. Then, we started practicing VMD ray tracing and learnt how to use Amazon as a high-performance tool providing GPUs. It was exciting to use virtual reality for structural biology. João V. Ribeiro presented a very useful talk about NAMD and displayed some aspects of launching MD simulation with it. On the hands-on part, I came up with how to access the PDC- Beskow & Tegner and how to use Slurm language for HPC and launching various jobs. On the third day, Erik demonstrated a wonderful session in GROMACS with MD introduction, theories and various considerations in MD running, and I got experience in preparation for Markov state Modeling by running a short ensemble of Alanine Dipeptide. I also got to attend Thomas’s talk on AMBER and tutorials on hydrogen bond analysis with CPPTRAJ.

During that wonderful course, I felt as I am a part of the scientific family because of the great atmosphere as we gathered for dinner in the University’s restaurant and enjoyed the very stunning cruise in the Baltic sea. Consequently, I have known a number of academics and professionals from different countries who have similar research interests. Finally, I would like to deeply thank PRACE/BioExcel team for giving me this chance to attend the school and supporting me with travel grants which motivated me a lot to pursue various resources of knowledge.

 

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