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dc.contributor.authorBolnykh, Viacheslav
dc.contributor.authorOlsen, Jógvan Magnus Haugaard
dc.contributor.authorMeloni, Simone
dc.contributor.authorBircher, Martin Peter
dc.contributor.authorIppoliti, Emiliano
dc.contributor.authorCarloni, Paolo
dc.contributor.authorRothlisberger, Ursula
dc.date.accessioned2019-09-13T10:50:14Z
dc.date.available2019-09-13T10:50:14Z
dc.date.issued2019-09-09
dc.description.abstractWe present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing GGA and hybrid exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling of up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.en_US
dc.description.sponsorshipDanish Council for Independent Research (DFF) Carlsberg Foundation Deutsche Forschungsgemeinschaft Swiss National Science Foundationen_US
dc.descriptionAccepted manuscript version. Published version in <i>Journal of Chemical Theory and Computation</i> available at <a href=https://doi.org/10.1021/acs.jctc.9b00424>https://doi.org/10.1021/acs.jctc.9b00424. </a>en_US
dc.identifier.citationBolnykh, V., Olsen, J.M.H., Meloni, S., Bircher, M.P., Ippoliti, E., Carloni, P. & Rothlisberger, U. (2019). Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC. <i>Journal of Chemical Theory and Computation</i>. https://doi.org/10.1021/acs.jctc.9b00424en_US
dc.identifier.cristinIDFRIDAID 1724023
dc.identifier.issn1549-9618
dc.identifier.issn1549-9626
dc.identifier.urihttps://hdl.handle.net/10037/16193
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.relation.journalJournal of Chemical Theory and Computation
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel/en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/642069/EU/High Performance Computing in Life Sciences, Engineering And Physics/HPC-LEAP/en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/RCN/SFF/262695/Norway/Hylleraas Centre for Quantum Molecular Sciences//en_US
dc.rights.accessRightsopenAccessen_US
dc.subjectVDP::Mathematics and natural science: 400::Chemistry: 440en_US
dc.subjectVDP::Matematikk og Naturvitenskap: 400::Kjemi: 440en_US
dc.titleExtreme Scalability of DFT-based QM/MM MD Simulations Using MiMiCen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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