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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0003-0603-5514
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2013 (Engelska)Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 29, nr 7, s. 845-854Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

Ort, förlag, år, upplaga, sidor
2013. Vol. 29, nr 7, s. 845-854
Nyckelord [en]
Force-Field, Free-Energy, Biomolecular Simulation, Dynamics, Model, Refinement, Transition, Efficient, Constant, Proteins
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
URN: urn:nbn:se:kth:diva-121462DOI: 10.1093/bioinformatics/btt055ISI: 000316695700004PubMedID: 23407358Scopus ID: 2-s2.0-84875592758OAI: oai:DiVA.org:kth-121462DiVA, id: diva2:618644
Forskningsfinansiär
EU, Europeiska forskningsrådet, 209825 258980VetenskapsrådetStiftelsen för strategisk forskning (SSF)Swedish e‐Science Research CenterEU, FP7, Sjunde ramprogrammeteSSENCE - An eScience CollaborationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
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QC 20130429

Tillgänglig från: 2013-04-29 Skapad: 2013-04-29 Senast uppdaterad: 2020-03-09Bibliografiskt granskad

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Pall, SzilardHess, BerkLindahl, Erik

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