The Gromacs team is limited in size and resources despite working on one of the most ubiquitous molecular dynamics packages out there.

Their tools are not perfect. An email server is used for asking questions. This takes away from the community and structure that a typical forum can assume. The messages later are archived and can be searched through – but cannot be clamped together like stackoverflow does. The website is equally dead – outdated comments and documentation is available on every corner. The code is available but it does not use any publicly available services such as github which could significantly simplify the development cycle, discussion, and issue creation. Yet most importantly, moving to services like github gives Gromacs access to a huge pool of competent programmers.

With all this code to be maintained and tested and optimised further for the latest hardware, why would gromacs want to handle analysis when packages such as MDAnalysis keep showing up? Gromacs tools are poorly described and tricky to use. They use inconsistent rules making them even harder to work out. I myself reported multiple bugs, with one being a small bug where you are told that the analysis step is done in ps, but in fact it is dependant on your own choice of unit. Tutorials from others are often your only way forward.

Just today I was trying to analyse my simulation and due to the bug reported above I calculated RMSD every 100 nanoseconds giving me just 5 frames. Yet, for some reason, the analysis lasted as long as computing it for all frames. This most likely means that Gromacs reads in every frame sequentially regardless of how many frames it jumps over. I imagine that there is an advantage in that all frames are “checked” during the analysis, but it is not reasonable to do this every time in every type of analysis.

MDAnalysis does not have this issue. It creates some kind of index file and is capable of browsing through the trajectory very quickly. Despite the package not being fully ready and having many small issues, it is a very promising and growing package.

Gromacs should adapt to the new age and embrace new tools and large open source community, rather than over ambitiously try to achieve everything itself. Instead, Gromacs could slowly transition its set of tools to MDAnalysis, experience which over time would help them to move the community to github.