charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

Simple item page
dc.contributor.authorWacha, Andras F.en
dc.contributor.authorLemkul, Justin A.en
dc.date.accessioned2024-01-08T21:08:32Zen
dc.date.available2024-01-08T21:08:32Zen
dc.date.issued2023-07-03en
dc.description.abstractCHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-coded data, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving the local internal geometry is directly applicable for analogous transformations of other force fields.en
dc.description.versionPublished versionen
dc.format.extentPages 4246-4252en
dc.format.extent7 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier14 (Article number)en
dc.identifier.doihttps://doi.org/10.1021/acs.jcim.3c00860en
dc.identifier.eissn1549-960Xen
dc.identifier.issn1549-9596en
dc.identifier.issue14en
dc.identifier.orcidLemkul, Justin [0000-0001-6661-8653]en
dc.identifier.pmid37399236en
dc.identifier.urihttps://hdl.handle.net/10919/117317en
dc.identifier.volume63en
dc.language.isoenen
dc.publisherAmerican Chemical Societyen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/37399236en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectNucleic-Acidsen
dc.subjectSimulationsen
dc.subjectWateren
dc.subjectGUIen
dc.subjectParametrizationen
dc.subjectOptimizationen
dc.subjectDynamicsen
dc.subjectUpdateen
dc.subjectModelen
dc.subjectRNAen
dc.subject.meshAlgorithmsen
dc.subject.meshSoftwareen
dc.subject.meshMolecular Dynamics Simulationen
dc.titlecharmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACSen
dc.title.serialJournal of Chemical Information and Modelingen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

Files

Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
charmm2gmx An Automated Method to Port the CHARMM Additive Force Field to GROMACS.pdf
Size:
1.64 MB
Format:
Adobe Portable Document Format
Description:
Published version
Download
Name:
SupportingInformation_v11.docx
Size:
927.59 KB
Format:
Microsoft Word XML
Description:
Supporting information
Download
License bundle
Now showing 1 - 1 of 1
Name:
license.txt
Size:
1.5 KB
Format:
Plain Text
Description:
Download

Collections

All Faculty Deposits
Scholarly Works, Biochemistry