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{{Short description|Open-sourced format designed to simulate chemical properties}}
{{Infobox software
{{Infobox software
| name = GROMACS
| name = GROMACS
| logo = GROMACS logo.png
| logo = [[File:Gmx_logo_blue.png|250px]]
| screenshot =
| screenshot =
| caption =
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| author =
| caption =
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| developer = [[University of Groningen]]<br />[[Royal Institute of Technology]]<br />[[Uppsala University]]<ref>{{Cite web |url=http://www.gromacs.org/About_Gromacs/People |title=The GROMACS development team |access-date=2012-06-27 |archive-date=2020-02-26 |archive-url=https://web.archive.org/web/20200226063101/http://www.gromacs.org/About_Gromacs/People |url-status=dead }}</ref>
⚫
| author =
⚫
| released = {{Start date and age|1991}}
⚫
| developer = [[University of Groningen]]<br />[[Royal Institute of Technology]]<br />[[Uppsala University]]<ref>[http://www.gromacs.org/About_Gromacs/People The GROMACS development team]</ref>
⚫
| latest release version = 2024.2
⚫
| released = {{Start date and age|1991}}
⚫
| latest release date = {{Start date and age|2024|05|10|df=yes}}<ref name="manual">{{cite web |url= https://manual.gromacs.org/documentation/current/download.html |title= Downloads&nbsp;— GROMACS 2024.2 documentation |publisher= gromacs.org |access-date= 2024-05-24}}</ref>
⚫
| latest release version = 2021
| latest preview version =
⚫
| latest release date = {{Start date and age|2021|01|28|df=yes}}<ref>{{cite web |url= http://manual.gromacs.org/documentation/current/download.html |title= Gromacs Downloads |publisher= gromacs.org |access-date= 2020-08-14}}</ref>
| latest preview date =
| status = Active
| programming language = [[C++]], [[C (programming language)|C]], [[CUDA]], [[OpenCL]]
| programming language = [[C++]], [[C (programming language)|C]], [[CUDA]], [[OpenCL]], [[SYCL]]
| operating system = [[Linux]], [[macOS]], [[Microsoft Windows|Windows]], any other [[Unix]] variety
| operating system = [[Linux]], [[macOS]], [[Microsoft Windows|Windows]], any other [[Unix]] variety
| platform = Many
| platform = Many
| size =
| size =
| language = English
| language = English
| genre = [[Molecular dynamics]] simulation
| genre = [[Molecular dynamics]] simulation
| license = [[GNU Lesser General Public License|LGPL]] versions >= 4.6,<br />[[GNU General Public License|GPL]] versions < 4.6<ref name="About Gromacs">{{cite web |url= http://www.gromacs.org/About_Gromacs |title= About Gromacs |publisher= gromacs.org |date= 16 August 2010 |access-date= 2012-06-26}}</ref>
| license = [[GNU Lesser General Public License|LGPL]] versions >= 4.6<ref name="About GROMACS">{{cite web |url= https://www.gromacs.org/about.html |title= About GROMACS |publisher= gromacs.org |date= 17 May 2021 |access-date= 2024-05-24}}</ref>,<br />[[GNU General Public License|GPL]] versions < 4.6<ref name="About Gromacs">{{cite web |url= http://www.gromacs.org/About_Gromacs |title= About Gromacs |publisher= gromacs.org |date= 16 August 2010 |access-date= 2012-06-26 |archive-date= 2020-11-27 |archive-url= https://web.archive.org/web/20201127061817/http://www.gromacs.org/About_Gromacs |url-status= dead }}</ref>
| website = {{URL|www.gromacs.org}}
| website = {{URL|https://www.gromacs.org/}}
}}
}}


'''GROMACS''' is a [[molecular dynamics]] package mainly designed for simulations of [[protein]]s, [[lipid]]s, and [[nucleic acid]]s. It was originally developed in the Biophysical Chemistry department of [[University of Groningen]], and is now maintained by contributors in universities and research centers worldwide.<ref>{{cite web |url= http://www.gromacs.org/About_Gromacs/People |title= People&nbsp;— Gromacs |publisher= gromacs.org |date= 14 March 2012 |access-date= 26 June 2012}}</ref><ref name="pmid16211538">{{cite journal |vauthors=Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ |title= GROMACS: fast, flexible, and free |journal= J Comput Chem |volume= 26 |issue= 16 |pages= 1701–18 |year= 2005 |pmid= 16211538 |doi= 10.1002/jcc.20291|s2cid= 1231998 }}</ref><ref name="Hess_2008">{{cite journal |vauthors=Hess B, Kutzner C, Van Der Spoel D, Lindahl E |title= GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation |journal= J Chem Theory Comput |volume= 4 |issue= 2 |pages= 435–447 |year= 2008 |doi= 10.1021/ct700301q|pmid= 26620784 |hdl= 11858/00-001M-0000-0012-DDBF-0 |hdl-access= free }}</ref> GROMACS is one of the fastest and most popular software packages available,<ref>{{cite journal |author1=Carsten Kutzner |author2=David Van Der Spoel |author3=Martin Fechner |author4=Erik Lindahl |author5=Udo W. Schmitt |author6=Bert L. De Groot |author7=Helmut Grubmüller |title= Speeding up parallel GROMACS on high-latency networks |journal= Journal of Computational Chemistry |year= 2007 |volume= 28 |issue= 12 |pages= 2075–2084 |doi= 10.1002/jcc.20703 |pmid= 17405124|hdl=11858/00-001M-0000-0012-E29A-0 |s2cid=519769 |hdl-access=free }}</ref><ref>{{cite journal |author1=Berk Hess |author2=Carsten Kutzner |author3=David van der Spoel |author4=Erik Lindahl |title= GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation |journal= Journal of Chemical Theory and Computation |year= 2008 |volume= 4 |issue= 3 |pages= 435–447 |doi= 10.1021/ct700301q |pmid= 26620784|hdl= 11858/00-001M-0000-0012-DDBF-0 |hdl-access= free }}</ref> and can run on [[central processing unit]]s (CPUs) and [[graphics processing unit]]s (GPUs).<ref>{{cite web |url= http://www.gromacs.org/Downloads/Installation_Instructions/GPUs |title= GPUs&nbsp;— Gromacs |publisher= gromacs.org |date= 20 January 2012 |access-date= 26 June 2012}}</ref> It is free, [[open-source software]] released under the [[GNU General Public License]] (GPL),<ref name="About Gromacs"/> and starting with version 4.6, the [[GNU Lesser General Public License]] (LGPL).
'''GROMACS''' is a [[molecular dynamics]] package mainly designed for simulations of [[protein]]s, [[lipid]]s, and [[nucleic acid]]s. It was originally developed in the Biophysical Chemistry department of [[University of Groningen]], and is now maintained by contributors in universities and research centers worldwide.<ref>{{cite web |url= http://www.gromacs.org/About_Gromacs/People |title= People&nbsp;— Gromacs |publisher= gromacs.org |date= 14 March 2012 |access-date= 26 June 2012 |archive-date= 26 February 2020 |archive-url= https://web.archive.org/web/20200226063101/http://www.gromacs.org/About_Gromacs/People |url-status= dead }}</ref><ref name="pmid16211538">{{cite journal |vauthors=Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ |title= GROMACS: fast, flexible, and free |journal= J Comput Chem |volume= 26 |issue= 16 |pages= 1701–18 |year= 2005 |pmid= 16211538 |doi= 10.1002/jcc.20291|s2cid= 1231998 }}</ref><ref name="Hess_2008">{{cite journal |vauthors=Hess B, Kutzner C, Van Der Spoel D, Lindahl E |title= GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation |journal= J Chem Theory Comput |volume= 4 |issue= 2 |pages= 435–447 |year= 2008 |doi= 10.1021/ct700301q|pmid= 26620784 |hdl= 11858/00-001M-0000-0012-DDBF-0 |s2cid= 1142192 |hdl-access= free }}</ref> GROMACS is one of the fastest and most popular software packages available,<ref>{{cite journal |author1=Carsten Kutzner |author2=David Van Der Spoel |author3=Martin Fechner |author4=Erik Lindahl |author5=Udo W. Schmitt |author6=Bert L. De Groot |author7=Helmut Grubmüller |title= Speeding up parallel GROMACS on high-latency networks |journal= Journal of Computational Chemistry |year= 2007 |volume= 28 |issue= 12 |pages= 2075–2084 |doi= 10.1002/jcc.20703 |pmid= 17405124|hdl=11858/00-001M-0000-0012-E29A-0 |s2cid=519769 |hdl-access=free }}</ref><ref>{{cite journal |author1=Berk Hess |author2=Carsten Kutzner |author3=David van der Spoel |author4=Erik Lindahl |title= GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation |journal= Journal of Chemical Theory and Computation |year= 2008 |volume= 4 |issue= 3 |pages= 435–447 |doi= 10.1021/ct700301q |pmid= 26620784|hdl= 11858/00-001M-0000-0012-DDBF-0 |s2cid=1142192 |hdl-access= free }}</ref> and can run on [[central processing unit]]s (CPUs) and [[graphics processing unit]]s (GPUs).<ref>{{cite web |url= https://manual.gromacs.org/2024.2/install-guide/index.html#gpu-support |title= Installation guide |publisher= gromacs.org |date= 10 May 2024 |access-date= 24 May 2024}}</ref> It is free, [[open-source software]] released under the [[GNU Lesser General Public License]] (LGPL)<ref name="About GROMACS"/> ([[GNU General Public License|GPL]] prior to Version 4.6).


==History==
==History==
Line 28: Line 30:


==Features==
==Features==
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.<ref name="About Gromacs"/> In addition, support for different [[force field (chemistry)|force fields]] makes GROMACS very flexible. It can be executed in parallel, using [[Message Passing Interface]] (MPI) or [[thread (computer science)|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.<ref>{{cite web |url= http://manual.gromacs.org/current/online/flow.html |title= GROMACS flow chart |publisher= gromacs.org |date= 18 January 2009 |access-date= 26 June 2012 |archive-url= https://web.archive.org/web/20100624071059/http://manual.gromacs.org/current/online/flow.html |archive-date= 24 June 2010 |url-status= dead }}</ref>
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.<ref name="About GROMACS"/> In addition, support for different [[force field (chemistry)|force fields]] makes GROMACS very flexible. It can be executed in parallel, using [[Message Passing Interface]] (MPI) or [[thread (computer science)|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.<ref>{{cite web |url= https://manual.gromacs.org/2024.2/user-guide/flow.html |title= Flow Chart&nbsp;— GROMACS 2024.2 documentation |publisher= gromacs.org |date= 10 May 2024 |access-date= 24 May 2024}}</ref>

OpenCL and CUDA are possible for actual GPUs of AMD, Intel, and Nvidia with great acceleration against CPU based runs since Version 5 or higher.
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,<ref>{{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 }}</ref> and, in Version 2023, GROMACS has CUDA<ref>Yousif, Ragheed Hussam, et al. "Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors through Computational Approaches." ''Sains Malaysiana'' 49.3 (2020): 517-525.

APA</ref>, OpenCL, and SYCL backends for running on GPUs of AMD, Apple, Intel, and Nvidia, often with great acceleration compared to CPU. <ref>{{cite web |url= https://www.gromacs.org/topic/heterogeneous_parallelization.html |title= Heterogeneous parallelization and GPU acceleration&nbsp;— GROMACS webpage |publisher= gromacs.org |date= 10 May 2024 |access-date= 24 May 2024}}</ref>


===Easter eggs===
===Easter eggs===
{{As of|2010|01}}, GROMACS' source code contains approximately 400 alternative acronyms 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 acronym caused offense.<ref>{{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}}</ref>
{{As of|2010|01}}, GROMACS' source code contains approximately 400 alternative [[backronym]]s 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.<ref>{{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}}</ref>


==Applications==
==Applications==
Under a non-GPL license, GROMACS is widely used in the [[Folding@home]] [[distributed computing]] project for simulations of [[protein folding]], where it the base code for the project's largest and most regularly used series of [[Folding@home cores|calculation cores]].<ref>{{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 }}</ref><ref>{{Cite book |author1=Adam Beberg |author2=Daniel Ensign |author3=Guha Jayachandran |author4=Siraj Khaliq |author5=Vijay Pande |title= Folding@home: Lessons From Eight Years of Volunteer Distributed Computing |journal= Parallel & Distributed Processing, IEEE International Symposium |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 }}</ref> EvoGrid, a distributed computing project to evolve [[artificial life]], also employs GROMACS.<ref>{{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}}</ref>
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 [[Folding@home cores|calculation cores]].<ref>{{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 }}</ref><ref>{{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 }}</ref> EvoGrid, a distributed computing project to evolve [[artificial life]], also employs GROMACS<ref>{{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}}</ref>.<ref>{{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}}</ref>


==See also==
==See also==
Line 63: Line 68:
==External links==
==External links==
* {{Official website|www.gromacs.org}}
* {{Official website|www.gromacs.org}}
* [http://www.nvidia.com/object/gromacs_on_tesla.html GROMACS on GPUs]
* [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]
* [http://timn.ho.ua/ccs Binaries of GROMACS 4.6.5 for Windows / Cygwin]
* 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]
* [http://www.bwhpc-c5.de/wiki/index.php/Gromacs GROMACS on the bwHPC Clusters in Germany]


{{Chemistry software}}
{{Chemistry software}}


⚫
[[Category:Molecular dynamics software]]
[[Category:Free software programmed in C]]
[[Category:Free software programmed in C]]
⚫
[[Category:Molecular dynamics software]]

Latest revision as of 17:28, 25 August 2024

GROMACS
Developer(s)University of Groningen
Royal Institute of Technology
Uppsala University[1]
Initial release1991; 33 years ago (1991)
Stable release
2024.2 / 10 May 2024; 4 months ago (2024-05-10)[2]
Repository
Written inC++, C, CUDA, OpenCL, SYCL
Operating systemLinux, macOS, Windows, any other Unix variety
PlatformMany
Available inEnglish
TypeMolecular dynamics simulation
LicenseLGPL versions >= 4.6[3],
GPL versions < 4.6[4]
Websitewww.gromacs.org

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide.[5][6][7] GROMACS is one of the fastest and most popular software packages available,[8][9] and can run on central processing units (CPUs) and graphics processing units (GPUs).[10] It is free, open-source software released under the GNU Lesser General Public License (LGPL)[3] (GPL prior to Version 4.6).

History

[edit]

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]

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

Features

[edit]

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.[3] 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.[11]

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,[12] and, in Version 2023, GROMACS has CUDA[13], OpenCL, and SYCL backends for running on GPUs of AMD, Apple, Intel, and Nvidia, often with great acceleration compared to CPU. [14]

Easter eggs

[edit]

As of January 2010, 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.[15]

Applications

[edit]

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.[16][17] EvoGrid, a distributed computing project to evolve artificial life, also employs GROMACS[18].[19]

See also

[edit]

References

[edit]
  1. ^ "The GROMACS development team". Archived from the original on 2020-02-26. Retrieved 2012-06-27.
  2. ^ "Downloads — GROMACS 2024.2 documentation". gromacs.org. Retrieved 2024-05-24.
  3. ^ a b c "About GROMACS". gromacs.org. 17 May 2021. Retrieved 2024-05-24.
  4. ^ "About Gromacs". gromacs.org. 16 August 2010. Archived from the original on 2020-11-27. Retrieved 2012-06-26.
  5. ^ "People — Gromacs". gromacs.org. 14 March 2012. Archived from the original on 26 February 2020. Retrieved 26 June 2012.
  6. ^ Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005). "GROMACS: fast, flexible, and free". J Comput Chem. 26 (16): 1701–18. doi:10.1002/jcc.20291. PMID 16211538. S2CID 1231998.
  7. ^ Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008). "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation". J Chem Theory Comput. 4 (2): 435–447. doi:10.1021/ct700301q. hdl:11858/00-001M-0000-0012-DDBF-0. PMID 26620784. S2CID 1142192.
  8. ^ Carsten Kutzner; David Van Der Spoel; Martin Fechner; Erik Lindahl; Udo W. Schmitt; Bert L. De Groot; Helmut Grubmüller (2007). "Speeding up parallel GROMACS on high-latency networks". Journal of Computational Chemistry. 28 (12): 2075–2084. doi:10.1002/jcc.20703. hdl:11858/00-001M-0000-0012-E29A-0. PMID 17405124. S2CID 519769.
  9. ^ Berk Hess; Carsten Kutzner; David van der Spoel; Erik Lindahl (2008). "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation". Journal of Chemical Theory and Computation. 4 (3): 435–447. doi:10.1021/ct700301q. hdl:11858/00-001M-0000-0012-DDBF-0. PMID 26620784. S2CID 1142192.
  10. ^ "Installation guide". gromacs.org. 10 May 2024. Retrieved 24 May 2024.
  11. ^ "Flow Chart — GROMACS 2024.2 documentation". gromacs.org. 10 May 2024. Retrieved 24 May 2024.
  12. ^ Páll S, Zhmurov A, Bauer P, Abraham M, Lundborg M, Gray A, Hess B, Lindahl E (2020). "Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS". J Chem Phys. 153 (13): 134110. arXiv:2006.09167. doi:10.1063/5.0018516. PMID 33032406.
  13. ^ Yousif, Ragheed Hussam, et al. "Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors through Computational Approaches." Sains Malaysiana 49.3 (2020): 517-525. APA
  14. ^ "Heterogeneous parallelization and GPU acceleration — GROMACS webpage". gromacs.org. 10 May 2024. Retrieved 24 May 2024.
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