Greetings, wanderer.
We are Vedran and Matea, two academics who are enthusiastic about scientific research, especially in the field of computational chemistry, and open-source software, especially Linux, Python, FreeBSD, LaTeX, and Markdown. We sometimes write about these and related topics on this blog.
Enjoy your stay.
Photo source: Bozhin Karaivanov (@murrayc) | Unsplash
The other day, I set up a machine using a fairly standard Fedora 43 Server installation with a WireGuard VPN tunnel to another machine running a fairly standard Arch Linux installation (of course).
When I tried to SSH from the Arch machine to the Fedora machine, the OpenSSH client would hang.
Photo source: Murray Campbell (@murrayc) | Unsplash
Klara Filek, a postdoctoral researcher at the Medical University of Graz, recently wrote an article about career orientation for young scientists for the Penkala Association blog. She makes many great points through the article, and I heartily recommend reading it, especially to current PhD students seeking future opportunities.
I would like to emphasize the two reasons that she mentioned why career guidance is so difficult in Croatian academia (translation mine):
- Limited experience of the mentors: Many mentors rely on their own experience in a system they are part of and know very well, and outside of which they often cannot help us much (depending, of course, on the field and personal affinities).
- The “academia-only” narrative: Continuing higher education and a doctorate seem to presuppose a postdoc position and a teaching career. In addition, a good number of academics I was (and still am) surrounded by are convinced that academia is the only place where you can be creative and flexible, which is not true and makes it difficult to explore other possibilities.
I thought quite a bit about both of these points, given that I am guiding Matea Turalija through her PhD journey and I am eager to help her with my acquired experience as much as I can. However, as Klara explained above, this is far from a trivial endeavor.
Photo source: Katerina (@kat_katerina) | Unsplash
GROMACS 2025.1 (doi:10.5281/zenodo.15006630) bugfix release came out on Tuesday with a few bugfixes. Among them is a fix for energy correction map (CMAP) parsing code, a feature which I introduced in 2025 release in preparation for adding a converted version of Amber ff19SB force field (doi:10.1021/acs.jctc.9b00591) to GROMACS.
The fix for the issue also added several tests to avoid future regressions. I like developing free and open-source software in general and GROMACS in particular; it feels a lot like the postdoc years in Heidelberg again. However, that was not the only change I proposed that got merged for the bugfix release.
Photo source: Markus Spiske (@markusspiske) | Unsplash
Over the last couple of weeks, there has been a lot of discussion about scientific research funding in the US. There are many changes, and it remains to be seen what will come out of it in the end. If some of the new policies stick around for a longer time, I have no doubt they will inspire discussions and considerations in the rest of the world, including Europe, as many of them in the US tend to do.
While science funding in the US is an important and interesting topic, I would like to say a couple of words regarding science funding that hits closer to home, namely in Croatia. Earlier this week, the Croatian Science Foundation (HrZZ) closed the project call for Installation Research Projects UIP-2025-02. This was the first project call of this type after 5 years, which is possibly the reason why the usual range of eligible scientists with a maximum of 7 years after obtaining the PhD degree was extended to a maximum of 10 years after it. The call still requires a minimum of 2 years of experience after the degree.
Photo source: Lemon Pepper Pictures (@lemonpepperpictures) | Unsplash
FreeBSD Ports provide editors/vscode with the latest stable version of Visual Studio Code and the FreeBSD Foundation provides an excellent guide how to install and use it. Unfortunately, the latest stable version of Visual Studio Code Remote - SSH still does not officially support FreeBSD, but only Linux, Windows, and macOS.
Photo source: Lautaro Andreani (@lautaroandreani) | Unsplash
As many readers of this blog are already aware, we make great use of GitHub Pages for hosting this website and several others. In particular, after FIDIT's inf2 server was finally decomissioned, Pages was the obvious choice for replacing the remaining services it offered.
Since the number and variety of applications and services hosted on inf2 server grew and diminished organically over time, what remained afterward was a collection of complex, but unrelated link hierarchies that had to be redirected to new locations (remember that Cool URIs don't change).
/homePhoto source: Julian Hochgesang (@julianhochgesang) | Unsplash
FreeBSD 14.0-RELEASE annoucement is immiment. Due to faster (re)boot and related improvements by Colin Percival, this version made headlines in tech media even before it got released, which got me interested in trying it out on some of our machines. I installed the first beta on one of our servers and shortly afterward reported an upgrade bug, which got fixed during the beta cycle and was shipped as an errata in 13.2-RELEASE-p4 and 12.4-RELEASE-p6.
I was following the subsequent pre-releases with great interest as well. The final FreeBSD 14.0-RELEASE brings Clang/LLVM 16.0 (which we use in scientific software development and course teaching), OpenSSL 3.0, OpenZFS 2.2, Lua configuration support in the boot loader, upgraded WireGuard in the kernel wg driver, and plenty of other changes that are relevant to our usage. I found it well worth the time it took to go through these changes and learn what to expect from the release.
Photo source: Darran Shen (@darranshen) | Unsplash
My employment as a research and teaching assistant at Faculty of Informatics and Digital Technologies (FIDIT for short), University of Rijeka (UniRi) ended last month with the expiration of the time-limited contract I had. This moment has marked almost two full years I spent in this institution and I think this is a good time to take a look back at everything that happened during that time. Inspired by the recent posts by the PI of my group, I decided to write my perspective on the time that I hope is just the beginning of my academic career.
Photo source: Jahanzeb Ahsan (@jahan_photobox) | Unsplash
This month we had Alumni Meeting 2023 at the Heidelberg Institute for Theoretical Studies, or HITS for short. I was very glad to attend this whole-day event and reconnect with my former colleagues as well as researchers currently working in the area of computational biochemistry at HITS. After all, this is the place and the institution where I worked for more than half of my time as a postdoc, where I started regularly contributing code to GROMACS molecular dynamics simulator, and published some of my best papers.
Photo source: Patrik Kernstock (@pkernstock) | Unsplash
Our everyday scientific and educational work relies heavily on hardware, software, and, in modern times, cloud services. The equipment that we will mention below is specific to our group; common services used by university and/or faculty employees will not be specifically mentioned here.
