GROMACS is a

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...

package mainly designed for simulations of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

lipid Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...

s, and

nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...

s. It was originally developed in the Biophysical Chemistry department of

University of Groningen The University of Groningen (abbreviated as UG; , abbreviated as RUG) is a Public university#Continental Europe, public research university of more than 30,000 students in the city of Groningen (city), Groningen, Netherlands. Founded in 1614, th ...

, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on

central processing unit A central processing unit (CPU), also called a central processor, main processor, or just processor, is the primary Processor (computing), processor in a given computer. Its electronic circuitry executes Instruction (computing), instructions ...

s (CPUs) and

graphics processing unit A graphics processing unit (GPU) is a specialized electronic circuit designed for digital image processing and to accelerate computer graphics, being present either as a discrete video card or embedded on motherboards, mobile phones, personal ...

s (GPUs). It is free,

open-source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

released under the GNU Lesser General Public License (LGPL) ( GPL prior to Version 4.6).

History

The GROMACS project originally began in 1991 at Department of Biophysical Chemistry,

Netherlands , Terminology of the Low Countries, informally Holland, is a country in Northwestern Europe, with Caribbean Netherlands, overseas territories in the Caribbean. It is the largest of the four constituent countries of the Kingdom of the Nether ...

(1991–2000). Its name originally derived from this time (GROningen MAchine for Chemical Simulations) although currently GROMACS is not an abbreviation for anything, as little active development has taken place in Groningen in recent decades. The original goal was to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture (since superseded by modern hardware designs). The molecular dynamics specific routines were rewritten in the programming language C from the Fortran 77-based program GROMOS, which had been developed in the same group. Since 2001, GROMACS is developed by the GROMACS development teams at the Royal Institute of Technology and

Uppsala University Uppsala University (UU) () is a public university, public research university in Uppsala, Sweden. Founded in 1477, it is the List of universities in Sweden, oldest university in Sweden and the Nordic countries still in operation. Initially fou ...

Sweden Sweden, formally the Kingdom of Sweden, is a Nordic countries, Nordic country located on the Scandinavian Peninsula in Northern Europe. It borders Norway to the west and north, and Finland to the east. At , Sweden is the largest Nordic count ...

Features

GROMACS is operated via the

command-line interface A command-line interface (CLI) is a means of interacting with software via command (computing), commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user ...

, and can use files for input and output. It provides calculation progress and estimated time of arrival (ETA) feedback, a trajectory viewer, and an extensive library for trajectory analysis. In addition, support for different force fields makes GROMACS very flexible. It can be executed in parallel, using

Message Passing Interface The Message Passing Interface (MPI) is a portable message-passing standard designed to function on parallel computing architectures. The MPI standard defines the syntax and semantics of library routines that are useful to a wide range of use ...

(MPI) or threads. It contains a script to convert molecular coordinates from

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

(PDB) files into the formats it uses internally. Once a configuration file for the simulation of several molecules (possibly including

solvent A solvent (from the Latin language, Latin ''wikt:solvo#Latin, solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a Solution (chemistry), solution. A solvent is usually a liquid but can also be a solid, a gas ...

) has been created, the simulation run (which can be time-consuming) produces a trajectory file, describing the movements of the atoms over time. That file can then be analyzed or visualized with several supplied tools. GROMACS has had GPU offload support since Version 4.5, originally limited to Nvidia GPUs. GPU support has been expanded and improved over the years, and, in Version 2023, GROMACS has CUDA, OpenCL, and SYCL backends for running on GPUs of AMD, Apple, Intel, and Nvidia, often with great acceleration compared to CPU.

Easter eggs

, GROMACS' source code contains approximately 400 alternative

backronym A backronym is an acronym formed from an already existing word by expanding its letters into the words of a phrase. Backronyms may be invented with either serious or humorous intent, or they may be a type of false etymology or folk etymology. The ...

s to ''GROMACS'' as jokes among the developers and

biochemistry Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...

researchers. These include "''Gromacs Runs On Most of All Computer Systems''", "''Gromacs Runs One Microsecond At Cannonball Speeds''", "''Good ROcking Metal Altar for Chronical Sinner''", "''Working on GRowing Old MAkes el Chrono Sweat''", and "''Great Red Owns Many ACres of Sand''". They are randomly selected to possibly appear in GROMACS's output stream. In one instance, such an bacronym, "''Giving Russians Opium May Alter Current Situation''", caused offense.

Applications

Under a non-GPL license, GROMACS is widely used in the Folding@home

distributed computing Distributed computing is a field of computer science that studies distributed systems, defined as computer systems whose inter-communicating components are located on different networked computers. The components of a distributed system commu ...

project for simulations of

protein folding Protein folding is the physical process by which a protein, after Protein biosynthesis, synthesis by a ribosome as a linear chain of Amino acid, amino acids, changes from an unstable random coil into a more ordered protein tertiary structure, t ...

, where it is the base code for the project's largest and most regularly used series of calculation cores. EvoGrid, a distributed computing project to evolve artificial life, also employs GROMACS.

References

External links