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It includes a preface and disclaimer, citation and release notes, and online resources for documentation and community support. The manual’s structure covers introductory topics such as computational chemistry and molecular dynamics, then proceeds through definitions and units, core algorithms, periodic boundary conditions, group concepts, molecular dynamics procedures, integrators, force computations, constraints, and related simulation methods.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":30,"@type":76,"position":81},"https://docshare.wps.com/document/technology/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/gromacs-user-manual-version-507/291351/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/gromacs-user-manual-version-507/291351.png","ImageObject",300,407,{"name":92,"@type":93},"Oliver Hayes","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-15","2026-09-17",true,{"@type":102,"interactionType":103,"userInteractionCount":44},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What version of the GROMACS manual is this?","Question",{"text":112,"@type":113},"The manual is version 5.0.7.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How should this manual be cited in scientific publications?",{"text":117,"@type":113},"Cite it as “GROMACS User Manual version 5.0.7” with the listed authors and the www.gromacs.org website, as specified in the citation section.",{"name":119,"@type":110,"acceptedAnswer":120},"What license applies to the GROMACS package?",{"text":121,"@type":113},"The GROMACS package is available under the GNU Lesser General Public License, version 2.1.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},291351,1790469322,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":29,"category_name":30,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":44,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},687207020761,"https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d","GROMACS  \nGroningen Machine for Chemical Simulations  \nUSER MANUAL  \nVersion 5.0.7  \nGROMACS USER MANUAL  \nVersion 5.0.7  \nContributions from  \nEmile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pr Bjelkmar, Rudi van Drunen, Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, Christoph Junghans, Jochen Hub, Peter Kasson, Carsten Kutzner, Brad Lambeth, Per Larsson, Justin A. Lemkul, Erik Marklund, Peiter Meulenhoff, Teemu Murtola, Szilrd Pll, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Christian Wennberg and Maarten Wolf.  \nMark Abraham, Berk Hess, David van der Spoel, and Erik  \nLindahl.  \n􀀍c 1991–2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands.  \n􀀍c 2001–2015: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden.  \n[More information can be found on our website:](More information can be found on our website: www.gromacs.org)[ www.gromacs.org](More information can be found on our website: www.gromacs.org).  \nPreface & Disclaimer  \nThis manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is worked on continuously, which in some cases might mean the information is not entirely correct.  \nComments on form and content are welcome, please send them to one of the mailing lists (see [www.gromacs.org](www.gromacs.org)), [or open an issue at](or open an issue at redmine.gromacs.org. Corrections)[ redmine.gromacs.org](or open an issue at redmine.gromacs.org. Corrections)[. Corrections](or open an issue at redmine.gromacs.org. Corrections) can also be made in the GROMACS git [source repository and uploaded to](source repository and uploaded to gerrit.gromacs.org)[ gerrit.gromacs.org](source repository and uploaded to gerrit.gromacs.org).  \nWe release an updated version of the manual whenever we release a new version of the software, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation.  \nOn-line Resources  \nYou can fi[nd more documentation and other material at our homepage](nd more documentation and other material at our homepage www.gromacs.org. Among)[ www.gromacs.org](nd more documentation and other material at our homepage www.gromacs.org. Among)[. Among](nd more documentation and other material at our homepage www.gromacs.org. Among)[ ](nd more documentation and other material at our homepage www.gromacs.org. Among)[other things there is an on-line reference](other things there is an on-line reference), [several GROMACS mailing lists with archives and](several GROMACS mailing lists with archives and)[ ](several GROMACS mailing lists with archives and)[contributed topologies/force](contributed topologies/force) fi[elds](elds).  \nCitation information  \nWhen citing this document in any scientific publication please refer to it as:  \nM.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team, GROMACS User Manual version 5.0.7, [www.gromacs.org](www.gromacs.org)[ ](www.gromacs.org)(2015)  \nHowever, we prefer that you cite (some of) the GROMACS papers [1, 2, 3, 4, 5, 6, 7, 8] when you publish your results. Any future development depends on academic research grants, since the package is distributed as free software!  \nGROMACS is Free Software  \nThe entire GROMACS package is available under the GNU Lesser General Public License, version 2.1. This means it's free as in free speech, not just that you can use it without paying us money. For details, check the COPYING file in the source code or consult [http://www.gnu.org/licenses/old](http://www.gnu.org/licenses/old)licenses/lgpl-2.1.html.  \nThe GROMACS source code and and selected set of binary packages are available on our homepage, [www.gromacs.org](www.gromacs.org. Have fun)[. Have fun](www.gromacs.org. Have fun).  \nContents  \n1 Introduction 1","cbCaitrY3RYj7ZMD","https://ap.wps.com/l/cbCaitrY3RYj7ZMD","pdf",11996978,310,"English","# Introduction\n## Computational Chemistry and Molecular Modeling\n## Molecular Dynamics Simulations\n## Energy Minimization and Search Methods\n# Definitions and Units\n## Notation\n## MD units\n## Reduced units\n# Algorithms\n## Periodic boundary conditions\n## The group concept\n## Molecular Dynamics\n## Constraint algorithms","[{\"question\":\"What version of the GROMACS manual is this?\",\"answer\":\"The manual is version 5.0.7.\"},{\"question\":\"How should this manual be cited in scientific publications?\",\"answer\":\"Cite it as “GROMACS User Manual version 5.0.7” with the listed authors and the www.gromacs.org website, as specified in the citation section.\"},{\"question\":\"What license applies to the GROMACS package?\",\"answer\":\"The GROMACS package is available under the GNU Lesser General Public License, version 2.1.\"}]","GROMACS User Manual - Version 5.0.7 | PDF",1789644938,781]