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This is academia; everybody has to get something

A tree in the middle of a snowy field

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 write about how I ended up working on molecular simulations and scientific software after 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.

  • u Computing
  • 12 minut(a/e) čitanja

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

opened brown wooden window

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.

  • u Computing
  • 3 minut(a/e) čitanja

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

white car parked in front of store during night time

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.

  • u Computing
  • 6 minut(a/e) čitanja

Coming /home

brown wooden chair beside white wall

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.

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

a fountain in the middle of a town square

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.

Don't use RAR

a large white tank

Photo source: Tim Mossholder (@ctimmossholder) | Unsplash

I sometimes joke with my TA Milan Petrović that his usage of RAR does not imply that he will be driving a rari. After all, he is not Devito rapping^Wsinging Uh 😤. Jokes aside, if you search for "should I use RAR" or a similar phrase on your favorite search engine, you'll see articles like 2007 Don't Use ZIP, Use RAR and 2011 Why RAR Is Better Than ZIP & The Best RAR Software Available.

  • u Computing
  • 2 minut(a/e) čitanja

Enabling HTTP/2, HTTPS, and going HTTPS-only on inf2

an old padlock on a wooden door

Photo source: Arkadiusz Gąsiorowski (@ambuscade) | Unsplash

Inf2 is a web server at University of Rijeka Department of Informatics, hosting Sphinx-produced static HTML course materials (mirrored elsewhere), some big files, a WordPress instance (archived elsewhere), and an internal instance of Moodle.

HTTPS was enabled on inf2 for a long time, albeit using a self-signed certificate. However, with Let's Encrpyt coming into public beta, we decided to join the movement to HTTPS.