Latest blog posts

Cross-building and cross-testing GROMACS for Windows on Linux with MinGW and Wine

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.

The unfortunate state of early-career scientist funding in Croatia

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.

How to run Visual Studio (VS) Code Remote over SSH on FreeBSD 13 and 14

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.

Serverless URL redirects using JavaScript on GitHub Pages

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).

Coming /home

Photo 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.

My perspective after two years as a research and teaching assistant at FIDIT

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.

Alumni Meeting 2023 at HITS and the reminiscence of the postdoc years

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.

What hardware, software, and cloud services do we use?

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.

Should I do a Ph.D.?

Photo source: Santeri Liukkonen (@iamsanteri) | Unsplash

Tough question, and the one that has been asked and answered over and over. The simplest answer is, of course, it depends on many factors.

As I started blogging at the end of my journey as a doctoral student, the topic of how I selected the field and ultimately decided to enroll in the postgraduate studies never really came up. In the following paragraphs, I will give a personal perspective on my Ph.D. endeavor. Just like other perspectives from doctors of not that kind, it is specific to the person in the situation, but parts of it might apply more broadly.

Publishing (Material for) MkDocs website to GitHub Pages using custom Actions workflow

Photo source: Roman Synkevych (@synkevych) | Unsplash

As you can probably see, this website is built using the Material theme for MkDocs, which we have been happily using for over one year after using Sphinx for many years prior to that. GitHub Pages offers built-in support for Jekyll, but not for MkDocs and therefore it requires the manual building and deployment of our website. However, it automates many other things, including HTTPS certificate provisioning on our domain via Let's Encrypt.

There are several somewhat related approaches using GitHub Actions for automating the deployment of MkDocs-generated sites, usually with the Material theme, to GitHub Pages. These guides are not only found on blogs written by enthusiasts; the official Getting started section of the Material for MkDocs documentation describes the usage of GitHub Actions for deployment and provides a generic YAML file for that purpose.