PMX is a free, open-source tool for setting up and analysing alchemical free-energy calculations with GROMACS. It automates the generation of hybrid structures and molecular topologies for studying mutations and ligand-binding changes, supporting applications in biomolecular research and computer-aided drug discovery.

ESPResSo is an open-source molecular dynamics package for simulating and analysing coarse-grained soft-matter systems. It supports research on polymers, liquid crystals, colloids, ferrofluids, and biological materials such as DNA and lipid membranes.

HADDOCK (High Ambiguity Driven protein–protein DOCKing) is a data-driven computational platform developed by Alexandre Bonvin and the Computational Structural Biology group at Utrecht University. It predicts and models biomolecular complexes—such as protein–protein, protein–DNA, and protein–RNA interactions—by integrating experimental data with molecular modeling and docking methods.

A premier, deeply granular performance analysis tool. Computer scientists use it to optimize thread execution, memory access, and vectorization to ensure their code is extracting maximum theoretical performance from the underlying CPU/GPU architecture.

HPCToolkit analyzes program performance to pinpoint exact bottlenecks (e.g., CPU idle time, cache misses, memory overhead) across thousands of nodes without heavily slowing down the application during testing.

A deep learning optimization library that makes distributed training of massive AI models (like Large Language Models) possible. It manages memory and pipeline parallelism across thousands of GPUs on an HPC, solving the problem of models being too large to fit in a single machine's VRAM.

A container solution specifically designed for HPC systems. Unlike Docker, it does not require root privileges (enhancing security) and integrates seamlessly with underlying hardware (GPUs, Infiniband).

A state-of-the-art package manager built specifically for HPC. It allows researchers to install multiple software versions with different compilers (e.g., GCC, Intel) without them conflicting with one another.