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dc.contributor.authorJansen, Anton
dc.contributor.authorAho, Noora
dc.contributor.authorGroenhof, Gerrit
dc.contributor.authorBuslaev, Pavel
dc.contributor.authorHess, Berk
dc.date.accessioned2024-01-19T06:59:49Z
dc.date.available2024-01-19T06:59:49Z
dc.date.issued2024
dc.identifier.citationJansen, A., Aho, N., Groenhof, G., Buslaev, P., & Hess, B. (2024). phbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. <i>Journal of Chemical Information and Modeling</i>, <i> 64</i>(3), 567-574. <a href="https://doi.org/10.1021/acs.jcim.3c01313" target="_blank">https://doi.org/10.1021/acs.jcim.3c01313</a>
dc.identifier.otherCONVID_197945475
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/92887
dc.description.abstractConstant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.en
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherAmerican Chemical Society (ACS)
dc.relation.ispartofseriesJournal of Chemical Information and Modeling
dc.rightsCC BY 4.0
dc.subject.otherchemical structure
dc.subject.otherions
dc.subject.othermathematical methods
dc.subject.othermolecules
dc.subject.otherpeptides
dc.subject.otherproteins
dc.titlephbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-202401191383
dc.contributor.laitosKemian laitosfi
dc.contributor.laitosDepartment of Chemistryen
dc.contributor.oppiaineOrgaaninen kemiafi
dc.contributor.oppiaineNanoscience Centerfi
dc.contributor.oppiaineFysikaalinen kemiafi
dc.contributor.oppiaineOrganic Chemistryen
dc.contributor.oppiaineNanoscience Centeren
dc.contributor.oppiainePhysical Chemistryen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.type.coarhttp://purl.org/coar/resource_type/c_2df8fbb1
dc.description.reviewstatuspeerReviewed
dc.format.pagerange567-574
dc.relation.issn1549-9596
dc.relation.numberinseries3
dc.relation.volume64
dc.type.versionpublishedVersion
dc.rights.copyright© The Authors. Published by American Chemical Society
dc.rights.accesslevelopenAccessfi
dc.relation.grantnumber332743
dc.relation.grantnumber311031
dc.relation.grantnumber342908
dc.subject.ysomatemaattiset menetelmät
dc.subject.ysopeptidit
dc.subject.ysomolekyylit
dc.subject.ysoionit
dc.subject.ysoproteiinit
dc.format.contentfulltext
jyx.subject.urihttp://www.yso.fi/onto/yso/p1880
jyx.subject.urihttp://www.yso.fi/onto/yso/p15258
jyx.subject.urihttp://www.yso.fi/onto/yso/p2984
jyx.subject.urihttp://www.yso.fi/onto/yso/p9015
jyx.subject.urihttp://www.yso.fi/onto/yso/p4332
dc.rights.urlhttps://creativecommons.org/licenses/by/4.0/
dc.relation.doi10.1021/acs.jcim.3c01313
dc.relation.funderResearch Council of Finlanden
dc.relation.funderResearch Council of Finlanden
dc.relation.funderResearch Council of Finlanden
dc.relation.funderSuomen Akatemiafi
dc.relation.funderSuomen Akatemiafi
dc.relation.funderSuomen Akatemiafi
jyx.fundingprogramAcademy Project, AoFen
jyx.fundingprogramAcademy Project, AoFen
jyx.fundingprogramPostdoctoral Researcher, AoFen
jyx.fundingprogramAkatemiahanke, SAfi
jyx.fundingprogramAkatemiahanke, SAfi
jyx.fundingprogramTutkijatohtori, SAfi
jyx.fundinginformationThis research was supported by the Swedish Research Council (Grant 2019-04477), the Academy of Finland (Grants 311031, 332743, and 342908), and the Bio Excel CoE (Grants H2020-INFRAEDI-02-2018-823830 and 101093290).
dc.type.okmA1


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