Introductory Tutorials for Simulating Protein Dynamics with GROMACS

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dc.contributor.authorLemkul, Justin A.en
dc.date.accessioned2025-01-08T18:37:20Zen
dc.date.available2025-01-08T18:37:20Zen
dc.date.issued2024-09-21en
dc.description.abstractAtomistic molecular dynamics (MD) simulations have become an indispensable tool for investigating the structure, dynamics, and energetics of biomolecules. Continual optimization of software algorithms and hardware has enabled investigators to access biologically relevant time scales in feasible amounts of computing time. Given the widespread use and utility of MD simulations, there is considerable interest in learning essential skills in performing them. Here, we present a set of introductory tutorials for performing MD simulations of proteins in the popular, open-source GROMACS package. Three exercises are detailed, including simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. Essential features and input settings are illustrated throughout. The purpose of these tutorials is to provide new users with a general understanding of foundational workflows, from which they can design their own simulations.en
dc.description.versionPublished versionen
dc.format.extentPages 9418-9435en
dc.format.extent18 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1021/acs.jpcb.4c04901en
dc.identifier.eissn1520-5207en
dc.identifier.issn1520-6106en
dc.identifier.issue39en
dc.identifier.orcidLemkul, Justin [0000-0001-6661-8653]en
dc.identifier.pmid39305267en
dc.identifier.urihttps://hdl.handle.net/10919/123965en
dc.identifier.volume128en
dc.language.isoenen
dc.publisherAmerican Chemical Societyen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/39305267en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subject.meshProteinsen
dc.subject.meshAlgorithmsen
dc.subject.meshSoftwareen
dc.subject.meshMolecular Dynamics Simulationen
dc.titleIntroductory Tutorials for Simulating Protein Dynamics with GROMACSen
dc.title.serialJournal of Physical Chemistry Ben
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
pubs.organisational-groupVirginia Techen
pubs.organisational-groupVirginia Tech/Agriculture & Life Sciencesen
pubs.organisational-groupVirginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-groupVirginia Tech/All T&R Facultyen
pubs.organisational-groupVirginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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