Título:
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PARMBSC1: A refined force-field for DNA simulations
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Autor/a:
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Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balanceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluís; González, Carlos; Vendruscolo, Michele; Laughton, Charles A.; Harris, Sarah A.; Case, David A.; Orozco, Modesto
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Otros autores:
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Barcelona Supercomputing Center |
Abstract:
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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/. |
Abstract:
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MO thanks Spanish Ministry of Science (BIO2012-32868), the Catalan SGR, the Instituto Nacional de Bioinformática, and the European Research Council (ERC_SimDNA) for support. MO is an ICREA academia researcher. MO thanks CPU/GPU time on MareNostrum/MinoTauro (BSC). CAL, SAH and
AN thanks the UK HECBioSim Consortium for HPC time on ARCHER (Grant EP/L000253/1). AN was supported by the Biotechnology and Biological Sciences Research Council (BBSRC, grant number BB/I019294/1), and thanks ARC Leeds for computational resources. PDD is a PEDECIBA and SNI
(ANII, Uruguay) researcher. DAC thanks Chunmei Liu for assistance with the crystal simulation analysis. |
Abstract:
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Peer Reviewed |
Materia(s):
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-Àrees temàtiques de la UPC::Enginyeria mecànica -DNA--Analysis -Simulation methods -Computational biophysics -Computational models -DNA -ADN -Simulació, Mètodes de |
Derechos:
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Tipo de documento:
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Artículo - Versión presentada Artículo |
Editor:
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Nature Publishing Group
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