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Albaugh","year":"2016","journal-title":"J Phys Chem B"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"5430","DOI":"10.1021\/ct400781b","article-title":"Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator","volume":"9","author":"PEM Lopes","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"3579","DOI":"10.1080\/00268976.2013.844369","article-title":"Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps","volume":"111","author":"B Leimkuhler","year":"2013","journal-title":"Mol Phys"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"20160138","DOI":"10.1098\/rspa.2016.0138","article-title":"Efficient molecular dynamics using geodesic integration and solvent\u2013solute splitting","volume":"472","author":"B Leimkuhler","year":"2016","journal-title":"Proc R Soc 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Generalized Born","volume":"8","author":"AW G\u00f6tz","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"ref13","first-page":"41","article-title":"Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer","author":"DE Shaw","year":"2014","journal-title":"IEEE"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1021\/ct300857j","article-title":"OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation","volume":"9","author":"P Eastman","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"ref15","first-page":"399","article-title":"GPU Computing Gems Jade Edition","author":"P Eastman","year":"2012"},{"key":"ref16","unstructured":"Case DA, Betz RM, Botello-Smith W, Cerutti DS, Cheatham TE, Darden TA, et al. AMBER 2016 [Internet]. University of California, San Francisco; <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ambermd.org\" xlink:type=\"simple\">http:\/\/ambermd.org<\/ext-link>"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The biomolecular simulation program","volume":"30","author":"BR Brooks","year":"2009","journal-title":"J Comput Chem"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"MJ Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref19","doi-asserted-by":"crossref","unstructured":"Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, et al. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. Proceedings of the 2006 ACM\/IEEE Conference on Supercomputing. New York, NY, USA: ACM; 2006. 10.1145\/1188455.1188544","DOI":"10.1145\/1188455.1188544"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"NA","DOI":"10.1002\/prot.22711","article-title":"Improved side-chain torsion potentials for the Amber ff99SB protein force field","author":"K Lindorff-Larsen","year":"2010","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"WL Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"key":"ref22","unstructured":"Rizzi A, Grinaway PB, Parton DL, Shirts MR, Wang K, Eastman P, et al. YANK: A GPU-accelerated platform for alchemical free energy calculations [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/getyank.org\" xlink:type=\"simple\">http:\/\/getyank.org<\/ext-link>"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1063\/1.463137","article-title":"Reversible multiple time scale molecular dynamics","volume":"97","author":"M Tuckerman","year":"1992","journal-title":"J Chem Phys"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of State Calculations by Fast Computing Machines","volume":"21","author":"N Metropolis","year":"1953","journal-title":"J Chem Phys"},{"key":"ref25","article-title":"Free Energy Computations: A Mathematical Perspective","author":"T Lelievre","year":"2010"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"E1009","DOI":"10.1073\/pnas.1106094108","article-title":"Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation","volume":"108","author":"JP Nilmeier","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"4046","DOI":"10.1021\/ct4003702","article-title":"Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins","volume":"9","author":"Y Shi","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3368","DOI":"10.1063\/1.1777575","article-title":"Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics","volume":"121","author":"IR Craig","year":"2004","journal-title":"J Chem Phys"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3025","DOI":"10.1063\/1.1589749","article-title":"Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm","volume":"119","author":"G Lamoureux","year":"2003","journal-title":"J Chem Phys"},{"key":"ref30","doi-asserted-by":"crossref","DOI":"10.1063\/1.4873920","article-title":"An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald","volume":"140","author":"AC Simmonett","year":"2014","journal-title":"J Chem Phys"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/0009-2614(96)00952-9","article-title":"Recurrence relations for the direct calculation of spherical multipole interaction tensors and Coulomb-type interaction energies","volume":"260","author":"C H\u00e4ttig","year":"1996","journal-title":"Chem Phys Lett"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/0009-2614(80)80396-4","article-title":"Convergence acceleration of iterative sequences. the case of scf iteration","volume":"73","author":"P Pulay","year":"1980","journal-title":"Chem Phys Lett"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"74115","DOI":"10.1063\/1.4928530","article-title":"Efficient treatment of induced dipoles","volume":"143","author":"AC Simmonett","year":"2015","journal-title":"J Chem Phys"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.cplett.2005.10.135","article-title":"A polarizable model of water for molecular dynamics simulations of biomolecules","volume":"418","author":"G Lamoureux","year":"2006","journal-title":"Chem Phys Lett"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1002\/(SICI)1096-987X(19971130)18:15<1930::AID-JCC8>3.0.CO;2-P","article-title":"Unification of box shapes in molecular simulations","volume":"18","author":"H Bekker","year":"1997","journal-title":"J Comput Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.cpc.2012.09.022","article-title":"SPFP: Speed without compromise\u2014A mixed precision model for GPU accelerated molecular dynamics simulations","volume":"184","author":"S Le Grand","year":"2013","journal-title":"Comput Phys Commun"},{"key":"ref37","unstructured":"Swails J. ParmEd [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ParmEd\/ParmEd\" xlink:type=\"simple\">https:\/\/github.com\/ParmEd\/ParmEd<\/ext-link>"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","article-title":"CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM Simulations Using the CHARMM36 Additive Force Field","volume":"12","author":"J Lee","year":"2016","journal-title":"J Chem Theory Comput"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005659","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,8,9]],"date-time":"2017-08-09T00:00:00Z","timestamp":1502236800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005659","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T09:00:18Z","timestamp":1540285218000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005659"}},"subtitle":[],"editor":[{"given":"Robert","family":"Gentleman","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,26]]},"references-count":38,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2017,7,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005659","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/091801","asserted-by":"object"}],"has-review":[{"id-type":"doi","id":"10.3410\/f.727841100.793548462","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,26]]}}}