{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T19:16:32Z","timestamp":1772651792773,"version":"3.50.1"},"reference-count":28,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010582","name":"National Computational Infrastructure","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010582","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011025","name":"Government of Western Australia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["FL190100080"],"award-info":[{"award-number":["FL190100080"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computer Physics Communications"],"published-print":{"date-parts":[[2026,3]]},"DOI":"10.1016\/j.cpc.2025.110003","type":"journal-article","created":{"date-parts":[[2025,12,20]],"date-time":"2025-12-20T00:01:34Z","timestamp":1766188894000},"page":"110003","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Dofulator: A tool for calculating degrees of freedom of atoms in molecules with geometry constraints"],"prefix":"10.1016","volume":"320","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4097-0496","authenticated-orcid":false,"given":"Stephen","family":"Sanderson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3579-4747","authenticated-orcid":false,"given":"Sobin","family":"Alosious","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1346-8318","authenticated-orcid":false,"given":"Debra J.","family":"Searles","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"issue":"20","key":"10.1016\/j.cpc.2025.110003_bib0001","doi-asserted-by":"crossref","DOI":"10.1063\/5.0090983","article-title":"Thermal conductance of the water-gold interface: the impact of the treatment of surface polarization in non-equilibrium molecular simulations","volume":"156","author":"Olarte-Plata","year":"2022","journal-title":"J. Chem. Phys."},{"issue":"13-14","key":"10.1016\/j.cpc.2025.110003_bib0002","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1080\/08927022.2023.2232466","article-title":"Degrees of freedom of atoms in a rigid molecule for local temperature calculation in molecular dynamics simulation","volume":"49","author":"Matsubara","year":"2023","journal-title":"Mol. Simul."},{"issue":"23","key":"10.1016\/j.cpc.2025.110003_bib0003","doi-asserted-by":"crossref","first-page":"10615","DOI":"10.1021\/acs.jctc.4c00957","article-title":"Local temperature measurement in molecular dynamics simulations with rigid constraints","volume":"20","author":"Sanderson","year":"2024","journal-title":"J. Chem. Theory Comput."},{"issue":"10","key":"10.1016\/j.cpc.2025.110003_bib0004","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: a toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"Michaud-Agrawal","year":"2011","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.cpc.2025.110003_bib0005","series-title":"Proceedings of the 15th Python in Science Conference","doi-asserted-by":"crossref","DOI":"10.25080\/Majora-629e541a-00e","article-title":"MDAnalysis: a python package for the rapid analysis of molecular dynamics simulations","author":"Gowers","year":"2016"},{"issue":"8","key":"10.1016\/j.cpc.2025.110003_bib0006","doi-asserted-by":"crossref","first-page":"2581","DOI":"10.1021\/ct3002046","article-title":"Equipartition principle for internal coordinate molecular dynamics","volume":"8","author":"Jain","year":"2012","journal-title":"J. Chem. Theory Comput."},{"issue":"2","key":"10.1016\/j.cpc.2025.110003_bib0007","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1103\/PhysRevE.50.1559","article-title":"Generalized Euler equations for linked rigid bodies","volume":"50","author":"Kneller","year":"1994","journal-title":"Phys. Rev. E"},{"key":"10.1016\/j.cpc.2025.110003_bib0008","series-title":"Rigid Body Dynamics Algorithms","author":"Featherstone","year":"2008"},{"issue":"4","key":"10.1016\/j.cpc.2025.110003_bib0009","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1063\/1.479399","article-title":"Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion","volume":"111","author":"Mazur","year":"1999","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.cpc.2025.110003_bib0010","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"10.1016\/j.cpc.2025.110003_bib0011","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD \u2013 visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph"},{"key":"10.1016\/j.cpc.2025.110003_bib0012","series-title":"An Efficient Library for Parallel Ray Tracing and Animation","author":"Stone","year":"1998"},{"issue":"11","key":"10.1016\/j.cpc.2025.110003_bib0013","doi-asserted-by":"crossref","first-page":"5834","DOI":"10.1021\/acs.jctc.8b00768","article-title":"Automated topology builder version 3.0: prediction of solvation free enthalpies in water and hexane","volume":"14","author":"Stroet","year":"2018","journal-title":"J. Chem. Theory Comput."},{"issue":"12","key":"10.1016\/j.cpc.2025.110003_bib0014","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: a linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"issue":"7","key":"10.1016\/j.cpc.2025.110003_bib0015","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1007\/s00249-011-0700-9","article-title":"Definition and testing of the GROMOS force-field versions 54A7 and 54B7","volume":"40","author":"Schmid","year":"2011","journal-title":"Eur. Biophys. J."},{"issue":"5","key":"10.1016\/j.cpc.2025.110003_bib0016","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1063\/1.465041","article-title":"Constant pressure-constant temperature simulations of liquid water and carbon dioxide","volume":"98","author":"Palmer","year":"1993","journal-title":"J. Chem. Phys."},{"issue":"8","key":"10.1016\/j.cpc.2025.110003_bib0017","doi-asserted-by":"crossref","first-page":"3153","DOI":"10.1063\/1.476922","article-title":"Structural and thermodynamic properties of fluid carbon dioxide from a new ab initio potential energy surface","volume":"109","author":"Steinebrunner","year":"1998","journal-title":"J. Chem. Phys."},{"issue":"1","key":"10.1016\/j.cpc.2025.110003_bib0018","doi-asserted-by":"crossref","DOI":"10.1002\/wcms.1554","article-title":"WebMO: web-based computational chemistry calculations in education and research","volume":"12","author":"Polik","year":"2022","journal-title":"WIREs Comput. Mol. Sci."},{"key":"10.1016\/j.cpc.2025.110003_bib0019","series-title":"Technical Report","article-title":"Letter-Value Plots: Boxplots for Large Data","author":"Hofmann","year":"2011"},{"key":"10.1016\/j.cpc.2025.110003_bib0020","doi-asserted-by":"crossref","DOI":"10.1016\/j.cpc.2021.108171","article-title":"LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales","volume":"271","author":"Thompson","year":"2022","journal-title":"Comput. Phys. Commun."},{"issue":"24","key":"10.1016\/j.cpc.2025.110003_bib0021","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","article-title":"The missing term in effective pair potentials","volume":"91","author":"Berendsen","year":"1987","journal-title":"J. Phys. Chem."},{"issue":"2","key":"10.1016\/j.cpc.2025.110003_bib0022","doi-asserted-by":"crossref","DOI":"10.1063\/1.2136877","article-title":"Flexible simple point-charge water model with improved liquid-state properties","volume":"124","author":"Wu","year":"2006","journal-title":"J. Chem. Phys."},{"issue":"1","key":"10.1016\/j.cpc.2025.110003_bib0023","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0021-9991(83)90014-1","article-title":"Rattle: a \u201cvelocity\u201d version of the shake algorithm for molecular dynamics calculations","volume":"52","author":"Andersen","year":"1983","journal-title":"J. Comput. Phys."},{"issue":"20","key":"10.1016\/j.cpc.2025.110003_bib0024","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevB.81.205441","article-title":"Optimized Tersoff and Brenner empirical potential parameters for lattice dynamics and phonon thermal transport in carbon nanotubes and graphene","volume":"81","author":"Lindsay","year":"2010","journal-title":"Phys. Rev. B"},{"issue":"19","key":"10.1016\/j.cpc.2025.110003_bib0025","doi-asserted-by":"crossref","first-page":"13104","DOI":"10.1103\/PhysRevB.62.13104","article-title":"Carbon nanotubes, buckyballs, ropes, and a universal graphitic potential","volume":"62","author":"Girifalco","year":"2000","journal-title":"Phys. Rev. B"},{"issue":"6","key":"10.1016\/j.cpc.2025.110003_bib0026","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1021\/jp0268112","article-title":"On the water-carbon interaction for use in molecular dynamics simulations of graphite and carbon nanotubes","volume":"107","author":"Werder","year":"2003","journal-title":"J. Phys. Chem. B"},{"issue":"3","key":"10.1016\/j.cpc.2025.110003_bib0027","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1103\/PhysRevB.17.1302","article-title":"Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions","volume":"17","author":"Schneider","year":"1978","journal-title":"Phys. Rev. B"},{"issue":"03","key":"10.1016\/j.cpc.2025.110003_bib0028","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1142\/S0129183191001037","article-title":"Brownian dynamics simulations without Gaussian random numbers","volume":"02","author":"D\u00fcnweg","year":"1991","journal-title":"Int. J. Modern Phys. C"}],"container-title":["Computer Physics Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010465525005041?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010465525005041?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T17:33:56Z","timestamp":1772645636000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0010465525005041"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3]]},"references-count":28,"alternative-id":["S0010465525005041"],"URL":"https:\/\/doi.org\/10.1016\/j.cpc.2025.110003","relation":{},"ISSN":["0010-4655"],"issn-type":[{"value":"0010-4655","type":"print"}],"subject":[],"published":{"date-parts":[[2026,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Dofulator: A tool for calculating degrees of freedom of atoms in molecules with geometry constraints","name":"articletitle","label":"Article Title"},{"value":"Computer Physics Communications","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cpc.2025.110003","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"110003"}}