GROMACS

The GROMACS project originally began in 1991 at Department of Biophysical Chemistry, University of Groningen, Netherlands (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was to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture (since superseded by modern hardware designs).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.{{citation needed|date=June 2012}}

Since 2001, GROMACS is developed by the GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden.

GROMACS is operated via the command-line interface, 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 (MPI) or threads. It contains a script to convert molecular coordinates from Protein Data Bank (PDB) files into the formats it uses internally. Once a configuration file for the simulation of several molecules (possibly including solvent) 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.{{cite web |url= https://manual.gromacs.org/2024.2/user-guide/flow.html |title= Flow Chart — GROMACS 2024.2 documentation |publisher= gromacs.org |date= 10 May 2024 |access-date= 24 May 2024}}

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,{{cite journal |vauthors=Páll S, Zhmurov A, Bauer P, Abraham M, Lundborg M, Gray A, Hess B, Lindahl E |title=Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS |journal=J Chem Phys |volume=153 |issue=13 |pages=134110 |year= 2020 |pmid=33032406 |doi=10.1063/5.0018516 | doi-access= free|arxiv=2006.09167 |bibcode=2020JChPh.153m4110P }} 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. {{cite web |url= https://www.gromacs.org/topic/heterogeneous_parallelization.html |title= Heterogeneous parallelization and GPU acceleration — GROMACS webpage |publisher= gromacs.org |date= 10 May 2024 |access-date= 24 May 2024}}

{{As of|2010|01}}, GROMACS' source code contains approximately 400 alternative backronyms to GROMACS as jokes among the developers and biochemistry 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.{{cite web |url= http://foldingforum.org/viewtopic.php?f=16&t=12922#p126473 |title= Re: Working on Giving Russians Opium May Alter Current Situation |work= Folding@home |date= 17 January 2010 |access-date= 2012-06-26}}

Under a non-GPL license, GROMACS is widely used in the Folding@home distributed computing project for simulations of protein folding, where it is the base code for the project's largest and most regularly used series of calculation cores.{{cite web |url= http://folding.stanford.edu/English/FAQ-OpenSource |title= Folding@home Open Source FAQ |author= Pande lab |work= Folding@home |publisher= Stanford University |format= FAQ |date= 11 June 2012 |access-date= 26 June 2012 |url-status= dead |archive-url= https://web.archive.org/web/20120717063257/http://folding.stanford.edu/English/FAQ-OpenSource |archive-date= 17 July 2012 }}{{Cite book |author1=Adam Beberg |author2=Daniel Ensign |author3=Guha Jayachandran |author4=Siraj Khaliq |author5=Vijay Pande |title=2009 IEEE International Symposium on Parallel & Distributed Processing |chapter=Folding@home: Lessons from eight years of volunteer distributed computing |year= 2009 |pages= 1–8 |doi= 10.1109/IPDPS.2009.5160922 |issn= 1530-2075 |url= http://www.hicomb.org/papers/HICOMB2009-13.pdf |isbn= 978-1-4244-3751-1|s2cid=15677970 }} EvoGrid, a distributed computing project to evolve artificial life, also employs GROMACS.{{Cite web |title=Google Scholar |url=https://scholar.google.com/scholar?oi=bibs&hl=en&cluster=14833173061640186745 |access-date=2024-08-25 |website=scholar.google.com}}{{cite news |url= https://www.nytimes.com/2009/09/29/science/29grid.html?ref=science |title= Wanted: Home Computers to Join in Research on Artificial Life |last= Markoff |first= John |work= The New York Times |date= 29 September 2009 |access-date= 26 June 2012}}

{{Portal|Free and open-source software}}

{{Columns-list|colwidth=30em|

• OPLS
• GROMOS
• CHARMM
• NAMD
• Yasara
• Comparison of force field implementations
• Abalone (molecular mechanics)
• Grace (plotting tool)
• Folding@home
• Rosetta@home
• Comparison of software for molecular mechanics modeling
• Molecular design software
• OpenMM
• Bennett acceptance ratio
• VisIt
• VOTCA
• LAMMPS}}

{{Reflist|2}}

• {{Official website|www.gromacs.org}}
• [https://gromacs.bioexcel.eu/ GROMACS forums]
• Tutorials: [https://tutorials.gromacs.org/ official tutorials], [http://www.mdtutorials.com/gmx/ unofficial tutorial by Justin Lemkul], [https://gaseri.org/en/tutorials/gromacs/ unofficial tutorial by Wes Barnett], [https://wiki.bwhpc.de/e/GROMACS usage on the bwHPC Clusters in Germany]
• Specific versions: [https://www.nvidia.com/en-us/gpu-accelerated-applications/?search=gromacs GROMACS on GPUs by NVIDIA], [http://timn.ho.ua/ccs binaries of GROMACS 4.6.5 for Windows / Cygwin]

{{Chemistry software}}

Category:Free software programmed in C

Category:Molecular dynamics software