This is academia; everybody has to get something

Photo source: Lukas Seitz (@lukasseitz) | Unsplash

It has been three months since we published our preprint, and it has now passed 500 downloads. That seems like a good occasion to look back at a decision that gave me the opportunity to pursue this work: leaving a promising assistant professorship.

I have tried to write about that decision several times, but the drafts kept growing and none reached publication. There was always more to explain. This time, I will focus on what led to the decision and what came of it.

Initial conditions, real-world dynamics

One moment that stayed with me came at the Third Infinity conference in Göttingen in September 2022. I presented right after Anđela Šarić, whose group I follow and whose research I deeply admire. My presentation went fine, but I was struck by the scientific depth and scope of her work, brought to life through stunning visualizations. It made me ask what it would take for our group to produce work on that level and communicate it so effectively.

Even before that conference, we had tried to build a different setting for our scientific work. Through RxTx Research, Patrik Nikolić and I tried to bootstrap a business around free and open-source scientific software for drug discovery. Our work centered on RxDock, which we modernized and maintained for molecular docking and high-throughput virtual screening.¹ However, the effort did not, in the end, grow into a successful startup. There were several reasons, but, for now, I will simply say that too many of our assumptions proved wrong, both about the science and about building a business from Rijeka, Croatia, with limited access to the connections and capital we needed. Still, the attempt helped us recognize assumptions we had taken for granted and learn from putting them to the test.

On the academic side, I did not secure the Croatian Science Foundation funding I had sought, as I described in The unfortunate state of early-career scientist funding in Croatia. I could continue building the group with only basic funding or join an existing group at the University of Rijeka. Neither option seemed particularly appealing. I wanted to get back to doing the kind of science that had brought me to computational biochemistry in the first place.

Then, in April 2023, my mentor and longtime collaborator Željko Svedružić passed away unexpectedly, far too soon. Beyond the personal loss, this also meant that our years of scientific collaboration could not continue. The startup had not worked out, my attempt to establish an independently funded research group had not succeeded, and now I had lost the mentor with whom I had found my way into computational biochemistry. There was little left of the setting in which I had hoped to build my scientific work in Rijeka.

I began looking for a different setting in which to continue that work and applied for several positions. These were fixed-term roles below the assistant professor level, so leaving meant giving up both rank and security. Of the offers I received, I chose a position at the Max Planck Computing and Data Facility in Garching, where I had the opportunity to pick up almost exactly where I had left off in Heidelberg: as a computational biochemist and a member of the GROMACS developer community.

By the time I left for MPCDF in September 2023, I had spent twelve years at the University of Rijeka, teaching countless classes, mentoring students through their theses, and working to build a research group. Those years had given me relationships and responsibilities, not just a position. Leaving meant stepping away from a substantial part of my working life.

Other colleagues have pursued opportunities elsewhere, some before my departure and others since. Among those who already held PhDs, Igor Jugo moved into IT at KBC Rijeka and later into entrepreneurship, Dino Pitoski took a postdoctoral position at the University of Rijeka's Centre for Artificial Intelligence and Cybersecurity, and Draško Tomić joined the Ruđer Bošković Institute.

Other former research and teaching assistants pursued different paths: Luka Vretenar moved into industry, Maja Vrancich returned to school teaching, and Tomislav Slaviček-Car moved into entrepreneurship. Their circumstances differed, but their paths illustrate the range of possibilities beyond the faculty.

Back in the game with room to move

The preprint that prompted this reflection describes one substantial part of that work: porting the Amber ff14SB and ff19SB protein force fields to GROMACS. A force field specifies how the atoms in a simulation interact. The work also included the accompanying ion parameters and water models. Making these available in another simulation package might sound like a matter of translating parameter files, but reproducing their behavior requires more than copying the numbers.

For ff19SB, we needed to extend GROMACS to support amino-acid-specific corrections to the protein backbone's conformational energy. We also had to account for differences between Amber and GROMACS in fundamental constants, parameter precision, and even the ordering of atoms in improper dihedral interactions. My coauthors and I validated the converted force fields against Amber, comparing both individual interaction energies and the conformational behavior of ubiquitin in long simulations. The resulting force-field ports are now part of GROMACS, rather than a separate download that users have to find and assess themselves.

Alongside the force-field work, I have been helping keep GROMACS reliable as it evolves, from testing compatibility with newer C++ standards to enabling additional runtime checks and making compiler warnings more useful. That work also extends to scientific validation: ensuring that tests of argon and water still run under their intended conditions when simulation defaults change. The aim is not just to fix today's problems, but to make tomorrow's easier to detect.

Testing on different platforms is useful for the same reason. My work on Windows builds using MinGW and Wine exposed assumptions that were easy to miss elsewhere: trajectory-reading code could produce zero coordinates, while time-selection settings could leak between analysis-tool invocations within the same process. Supporting another platform is therefore not only about reaching its users. It can also reveal defects in code shared by everyone.

Other collaborations have taken me from using nuclear magnetic resonance measurements to improve simplified models of proteins to scaling GROMACS simulations to 65,536 CPU cores.

This combination of scientific questions and software development is what I had been looking for. I get to work on how we model molecular systems, turn that work into capabilities that other researchers can use, and help maintain the software on which those capabilities depend. I enjoy the everyday work, not just the prospect of a finished paper.

Academic conservation laws

My departure also meant a change for Matea Turalija, whose PhD I continue to supervise. Staying on as a teaching assistant at the Faculty of Informatics and Digital Technologies would, in practice, have meant finding another group willing to take her on and likely changing her PhD topic to fit its research. Instead, she moved to the Faculty of Medicine at the University of Rijeka, where she has more opportunities to deepen her understanding of the theoretical foundations of pharmacy and the computational methods and software used in drug research.

Her teaching now includes Informatics for Pharmacists, giving her another way to connect our computational biochemical work with pharmaceutical education. She is also part of a growing pharmacy programme, which has recently seen its first generation graduate and announced plans for an eventual independent faculty.

There were also different views of what the Faculty of Informatics and Digital Technologies should become. Some colleagues favored a more focused profile around applications of digital technologies in organizations and society, while I wanted computational biochemistry and other interdisciplinary research to have a larger place. Both were reasonable visions, even if they sometimes pulled decisions about the faculty's direction in different ways. In that sense, leaving made room for both: I could pursue computational biochemistry in a setting better suited to it, while they could continue developing their vision for the faculty.

Leaving did not mean taking the teaching materials with me. The colleagues who took over my courses have access to all the teaching and supporting materials we created, including those for Web Programming, Computer Systems Administration, Code Optimization, Computer Networks, and Informatics for Biotechnology. These remain openly available on this website, giving colleagues a starting point for reshaping the courses around their own expertise and interests rather than creating everything from scratch.

By maintaining teaching materials openly, we make it possible for the work to remain useful even when the person who wrote it moves elsewhere. Today's powerful AI agents offer another tool for colleagues who want to adapt and extend them.

For the teaching assistants I worked with, I hope my move also offered a useful example of what academic mobility can mean. It need not involve leaving permanently: Milan Petrović, for example, has undertaken research stays at ETH Zürich and Masaryk University, building collaborations around his research on social networks while continuing his PhD in Rijeka. What he gained was not a new institutional home, but a wider scientific circle. Whether my example had anything to do with it is a question for Milan, but I will gladly take a little credit anyway.

I am glad to stay in touch with former colleagues and other scientists in Croatia working in related fields, exchanging ideas and, when useful, offering advice based on my experience in Germany. My time in Heidelberg³ and Garching now adds up to more than five years of post-PhD research experience abroad. As a bonus, that experience also exceeds the four-year threshold in the Ministry's criteria for hiring returning scientists. Who knows whether that will ever come into play, but it leaves another possibility open for the future.

Looking back, I would say that everyone got something out of the change, even if it was not quite what we had originally planned. To adapt a line from Dragoslav “Car” in South Wind (srb. Južni vetar), this is the world of academia; everyone in it has to get something: some a fresh restart² and a new scientific home, others more room in the old one. Leaving did not mean that everything we had built had to end.

For my part, I gained the opportunity to do the scientific work I wanted to do. Giving up rank and security was a real cost, but I would make the same choice again.