Gromacs

GROMACS is a free, open-source software package for molecular dynamics simulations of biochemical systems. It is optimized for speed and scalability on multi-core CPUs and GPUs and is widely used to model proteins, nucleic acids, lipids, and other biomolecules.

Originating at the University of Groningen, where it stands for Groningen Machine for Chemical Simulations, GROMACS began in the 1990s under Erik van der Spoel and collaborators. It is distributed under the GNU General Public License and maintained by an international community.

Key features include a high-performance MD engine with velocity-Verlet integration, flexible thermostats and barostats, and long-range electrostatics via Particle Mesh Ewald. Bond constraints are handled by LINCS. It supports multiple force fields (GROMOS, AMBER, CHARMM, OPLS, MARTINI) and various water models, as well as all-atom and coarse-grained representations. Utilities such as grompp and mdrun prepare and execute simulations, and a suite of analysis tools handles energy, RMSD, hydrogen bonds, and more. File formats include .tpr, .gro, .top, and .xtc. GROMACS scales through MPI and OpenMP and offers GPU acceleration with CUDA and OpenCL; PME uses FFTW.

Applications span protein dynamics, folding, ligand binding, membrane systems, and materials science, making GROMACS a standard tool in computational chemistry and biophysics.

Availability and licensing: GROMACS is freely available under the GNU GPL, with ongoing development and documentation. It runs on Linux, macOS, and Windows and is supported by a large user and developer community.