title: Parmbsc1: a refined force field for DNA simulations.
abstract: We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Ivan
authors.initials: I
authors.lastname: Ivani
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Pablo D
authors.identifier: http://orcid.org/0000-0002-5927-372X
authors.initials: PD
authors.lastname: Dans
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds, UK.
authors.forename: Agnes
authors.initials: A
authors.lastname: Noy
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pérez
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Faustino
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Walther
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.|Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Pau
authors.initials: P
authors.lastname: Andrio
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.|Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Goñi
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Balaceanu
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.|Department of Chemistry, University of Cambridge, Cambridge, UK.
authors.forename: Guillem
authors.initials: G
authors.lastname: Portella
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
authors.forename: Federica
authors.initials: F
authors.lastname: Battistini
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.|Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
authors.forename: Josep Lluis
authors.identifier: http://orcid.org/0000-0002-0566-7723
authors.initials: JL
authors.lastname: Gelpí
authors.affiliation: Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
authors.forename: Carlos
authors.identifier: http://orcid.org/0000-0001-8796-1282
authors.initials: C
authors.lastname: González
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, UK.
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
authors.affiliation: School of Pharmacy, University of Nottingham, Nottingham, UK.|Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Laughton
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Harris
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.affiliation: Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.|Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.|Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D004247:DNA / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D004247:DNA