{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T15:10:09Z","timestamp":1789053009894,"version":"build-2803163510"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T00:00:00Z","timestamp":1785974400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":35,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Westf\u00e4lische Hochschule Gelsenkirchen Bocholt Recklinghausen"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>A fast pipeline based on the OPLS-AA force field is presented that enables the automated calculation of non-bonding intermolecular (dimer) interaction energies derived from a set of small organic (monomer) molecules. To calculate the non-bonding contributions, optimized geometries of the monomer molecules as well as their OPLS-AA van der Waals and atomic partial charge parameters are required. The key advantage of the new pipeline lies in its fast, highly parallelized in-memory computations without slow I\/O operations, which make it possible to thoroughly process comparatively large numbers of (more than a hundred) monomer molecules within acceptable time frames (hours and days): Compared to an analogous, more versatile, and comprehensive approach, the new computational scheme delivers comparable results while being more than two orders of magnitude faster. For locally estimating the required OPLS-AA force field parameters with the LigParGen and BOSS software packages, a user-friendly graphical user interface for the Windows operating system is provided.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Scientific contribution<\/jats:bold>\n                  <\/jats:p>\n                  <jats:p>Rapid calculation of mutual intermolecular energies for a set of monomer molecules based on the widely used OPLS-AA force field enables a considerable expansion of this type of calculation for practical purposes. The performance improvement can be used to achieve significant improvements of interaction energy averages as well as considerable expansions in the size of the monomer molecule set.<\/jats:p>","DOI":"10.1186\/s13321-026-01264-9","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T04:35:58Z","timestamp":1785990958000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fast intermolecular interaction energy calculation with the OPLS-AA force field"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8516-8974","authenticated-orcid":false,"given":"Mirco","family":"Daniel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5129-1298","authenticated-orcid":false,"given":"Hannah","family":"Kullik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6834-5714","authenticated-orcid":false,"given":"Martin","family":"Urban","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6966-0814","authenticated-orcid":false,"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0722-4229","authenticated-orcid":false,"given":"Achim","family":"Zielesny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,6]]},"reference":[{"key":"1264_CR1","doi-asserted-by":"publisher","DOI":"10.1002\/9783527806539","volume-title":"Chemoinformatics: basic concepts and methods","author":"T Engel","year":"2018","unstructured":"Engel T, Gasteiger J (2018) Chemoinformatics: basic concepts and methods. Wiley-VCH, Weinheim, Germany"},{"key":"1264_CR2","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199672394.001.0001","volume-title":"The theory of intermolecular forces","author":"AJ Stone","year":"2013","unstructured":"Stone AJ (2013) The theory of intermolecular forces, Second edition. Oxford University Press, Oxford, United Kingdom","edition":"Second edition"},{"key":"1264_CR3","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-024-00890-5","volume":"16","author":"F B\u00e4nsch","year":"2024","unstructured":"B\u00e4nsch F, Daniel M, Lanig H, Steinbeck C, Zielesny A (2024) An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package. J Cheminform 16:96. https:\/\/doi.org\/10.1186\/s13321-024-00890-5","journal-title":"J Cheminform"},{"issue":"1","key":"1264_CR4","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/s13321-024-00890-5","volume":"16","author":"F B\u00e4nsch","year":"2024","unstructured":"Mesoscopic Interaction Parameter Estimation with Tinker (MIPET). GitHub repository. https:\/\/github.com\/zielesny\/MIPET. Accessed on 10 Apr 2026","journal-title":"J Cheminf."},{"key":"1264_CR5","doi-asserted-by":"publisher","first-page":"5273","DOI":"10.1021\/acs.jctc.8b00529","volume":"14","author":"JA Rackers","year":"2018","unstructured":"Rackers JA, Wang Z, Lu C et al (2018) Tinker 8: software tools for molecular design. J Chem Theory Comput 14:5273\u20135289. https:\/\/doi.org\/10.1021\/acs.jctc.8b00529","journal-title":"J Chem Theory Comput"},{"key":"1264_CR6","doi-asserted-by":"publisher","first-page":"1657","DOI":"10.1021\/ja00214a001","volume":"110","author":"WL Jorgensen","year":"1988","unstructured":"Jorgensen WL, Tirado-Rives J (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657\u20131666. https:\/\/doi.org\/10.1021\/ja00214a001","journal-title":"J Am Chem Soc"},{"key":"1264_CR7","doi-asserted-by":"publisher","first-page":"11225","DOI":"10.1021\/ja9621760","volume":"118","author":"WL Jorgensen","year":"1996","unstructured":"Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225\u201311236. https:\/\/doi.org\/10.1021\/ja9621760","journal-title":"J Am Chem Soc"},{"key":"1264_CR8","unstructured":"LigParGen OPLS\/CM1A Parameter Generator for Organic Ligands. https:\/\/traken.chem.yale.edu\/ligpargen\/index.html. Accessed on 10 Apr 2026"},{"key":"1264_CR9","unstructured":"William L. Jorgensen Research Group. BOSS Homepage. https:\/\/zarbi.chem.yale.edu\/software.html . Accessed on 10 Apr 2026"},{"key":"1264_CR10","unstructured":"Jay Ponder Lab. Homepage.https:\/\/dasher.wustl.edu\/tinker\/distribution\/params\/ . Accessed on 10 Apr 2026"},{"key":"1264_CR11","unstructured":"Israel Cabeza de Vaca Lopez. LigParGen v2.1 repository on GitHub. https:\/\/github.com\/Isra3l\/ligpargen. Accessed on 10 Apr 2026"},{"issue":"W1","key":"1264_CR12","doi-asserted-by":"publisher","first-page":"W331","DOI":"10.1093\/nar\/gkx312","volume":"45","author":"LS Dodda","year":"2017","unstructured":"Dodda LS, Cabeza de Vaca I, Tirado-Rives J, Jorgensen WL (2017) LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Res 45(W1):W331\u2013W336. https:\/\/doi.org\/10.1093\/nar\/gkx312","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"1264_CR13","doi-asserted-by":"publisher","first-page":"3864","DOI":"10.1021\/acs.jpcb.7b00272","volume":"121","author":"LS Dodda","year":"2017","unstructured":"Dodda LS, Vilseck JZ, Tirado-Rives J, Jorgensen WL (2017) 1.14*CM1A-LBCC: localized bond-charge corrected CM1A charges for condensed-phase simulations. J Phys Chem B 121(15):3864\u20133870. https:\/\/doi.org\/10.1021\/acs.jpcb.7b00272","journal-title":"J Phys Chem B"},{"key":"1264_CR14","first-page":"3281","volume-title":"The encyclopedia of computational chemistry","author":"WL Jorgensen","year":"1998","unstructured":"Jorgensen WL (1998) BOSS - biochemical and organic simulation system. In: Schleyer PvR (ed) The encyclopedia of computational chemistry, vol 5. John Wiley & Sons Ltd, Athens, USA, pp 3281\u20133285"},{"issue":"16","key":"1264_CR15","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1002\/jcc.20297","volume":"26","author":"WL Jorgensen","year":"2005","unstructured":"Jorgensen WL, Tirado\u2013Rives J (2005) Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J Comput Chem 26(16):1689\u20131700. https:\/\/doi.org\/10.1002\/jcc.20297","journal-title":"J Comput Chem"},{"key":"1264_CR16","unstructured":"Python Software Foundation. Python 3.11. https:\/\/www.python.org\/downloads\/release\/python-3119\/. Accessed on 10 Apr 2026"},{"key":"1264_CR17","unstructured":"Riverbank Computing. PyQt. https:\/\/www.riverbankcomputing.com\/software\/pyqt\/ . Accessed on 10 Apr 2026"},{"issue":"19","key":"1264_CR18","doi-asserted-by":"publisher","first-page":"6665","DOI":"10.1073\/pnas.0408037102","volume":"102","author":"WL Jorgensen","year":"2005","unstructured":"Jorgensen WL, Tirado-Rives J (2005) Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci USA 102(19):6665\u20136670. https:\/\/doi.org\/10.1073\/pnas.0408037102","journal-title":"Proc Natl Acad Sci USA"},{"key":"1264_CR19","unstructured":"The ZeroMQ authors. ZeroMQ. https:\/\/zeromq.org\/ . Accessed on 10 Apr 2026"},{"key":"1264_CR20","unstructured":"The PyInstaller authors. PyInstaller. https:\/\/github.com\/pyinstaller\/pyinstaller. Accessed on 10 Apr 2026"},{"key":"1264_CR21","unstructured":"AlmaLinux OS Foundation. AlmaLinux Homepage. https:\/\/almalinux.org\/ . Accessed on 10 Apr 2026"},{"key":"1264_CR22","unstructured":"Jordan Russell and Martijn Laan. Inno Setup 6. https:\/\/jrsoftware.org\/isinfo.php . Accessed on 10 Apr 2026"},{"key":"1264_CR23","unstructured":"LigParGen-GUI repository on GitHub. https:\/\/github.com\/urban233\/LigParGen-GUI . Accessed on 10 Apr 2026"},{"key":"1264_CR24","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00432-9","volume":"12","author":"K van den Broek","year":"2020","unstructured":"van den Broek K, Daniel M, Epple M, Hein JM, Kuhn H, Neumann S, Truszkowski A, Zielesny A (2020) MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation. J Cheminform 12:29. https:\/\/doi.org\/10.1186\/s13321-020-00432-9","journal-title":"J Cheminform"},{"key":"1264_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-018-0278-7","volume":"10","author":"K van den Broek","year":"2018","unstructured":"van den Broek K, Kuhn H, Zielesny A (2018) Jdpd: an open Java simulation kernel for molecular fragment dissipative particle dynamics. J Cheminform 10:25. https:\/\/doi.org\/10.1186\/s13321-018-0278-7","journal-title":"J Cheminform"},{"issue":"305","key":"1264_CR26","doi-asserted-by":"publisher","DOI":"10.1016\/j.fuel.2021.121564","volume":"1","author":"AP Pinheiro","year":"2021","unstructured":"MFSim repository on GitHub. https:\/\/github.com\/zielesny\/MFsim . Accessed on 10 Apr 2026","journal-title":"Fuel"},{"issue":"6","key":"1264_CR27","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevApplied.19.064025","volume":"19","author":"L Di Palma","year":"2023","unstructured":"Jdpd repository on GitHub. https:\/\/github.com\/zielesny\/Jdpd. Accessed on 10 Apr 2026","journal-title":"Phys Rev Appl"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-026-01264-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-026-01264-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-026-01264-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T14:49:00Z","timestamp":1789051740000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13321-026-01264-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,6]]},"references-count":27,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1264"],"URL":"https:\/\/doi.org\/10.1186\/s13321-026-01264-9","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,6]]},"assertion":[{"value":"17 April 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"AZ is co-founder of GNWI\u2013Gesellschaft f\u00fcr naturwissenschaftliche Informatik mbH, Dortmund, Germany.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"128"}}