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Chem."},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","volume":"65","author":"Hornak V.","year":"2006","journal-title":"Proteins: Struc., Funct., and Bioinformatics"},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.sbi.2008.01.003","volume":"18","author":"Chen J.","year":"2008","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"Jorgensen W. L.","year":"1983","journal-title":"J. Chem. Phys."},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1021\/ja00392a016","volume":"103","author":"JORGENSEN W. L.","year":"1981","journal-title":"J. Am. Chem. Soc."},{"key":"ref13\/cit13","first-page":"6269","volume":"91","author":"Berendsen H. J. C.","year":"1987","journal-title":"J. Comput. Chem."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/nature12162","volume":"497","author":"Zhao G.","year":"2013","journal-title":"Nature"},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.str.2005.11.014","volume":"14","author":"Freddolino P. L.","year":"2006","journal-title":"Structure"},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/B978-0-12-394292-0.00007-2","volume":"523","author":"Kiss G.","year":"2013","journal-title":"Methods in Protein Design"},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"Hess B.","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"Phillips J. C.","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/jcc.540040211","volume":"4","author":"Brooks B. R.","year":"1983","journal-title":"J. Comput. Chem."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1086\/177668","volume":"468","author":"Fukushige T.","year":"1996","journal-title":"Astrophysics"},{"key":"ref21\/cit21","first-page":"244","author":"Sumanth J. V.","year":"2003","journal-title":"J. Parallel Distr. Com."},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1145\/1364782.1364802","volume":"51","author":"Shaw D. E.","year":"2008","journal-title":"Communications of the ACM"},{"key":"ref23\/cit23","doi-asserted-by":"crossref","unstructured":"Shaw, D. E. 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Chem."},{"key":"ref28\/cit28","first-page":"5342","volume":"227","author":"Anderson J. A.","year":"2008","journal-title":"J. Chem. Phys."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1177\/109434209601000401","volume":"10","author":"Nelson M. T.","year":"1996","journal-title":"International Journal of High Performance Computing Applications"},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1126\/science.282.5389.740","volume":"282","author":"Duan Y.","year":"1998","journal-title":"Science"},{"key":"ref31\/cit31","first-page":"327","volume":"23","author":"Ryckaert J.-P.","year":"1977","journal-title":"J. Chem. Phys."},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1021\/ct700200b","volume":"4","author":"Hess B.","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0010-4655(91)90021-C","volume":"67","author":"Liem S. Y.","year":"1991","journal-title":"Comput. Phys. Commun."},{"key":"ref34\/cit34","first-page":"300","volume":"16","author":"Bowers K. J.","year":"2005","journal-title":"J. Phys.: Conf. Ser."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"184109","DOI":"10.1063\/1.2191489","volume":"124","author":"Bowers K. J.","year":"2006","journal-title":"J. Chem. Phys."},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"121102","DOI":"10.1063\/1.2719690","volume":"126","author":"Meloni S.","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"4983","DOI":"10.1103\/PhysRevLett.86.4983","volume":"86","author":"Shirts M. R.","year":"2001","journal-title":"Phys. Rev. Lett."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.ymeth.2010.06.002","volume":"52","author":"Pande V. S.","year":"2010","journal-title":"Methods"},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"204909","DOI":"10.1063\/1.2116947","volume":"123","author":"Singhal N.","year":"2005","journal-title":"J. Chem. Phys."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"6571","DOI":"10.1021\/jp037421y","volume":"108","author":"Swope W. C.","year":"2004","journal-title":"J. Phys. Chem. B"},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S0006-3495(96)79552-8","volume":"70","author":"Huber G. A.","year":"1996","journal-title":"Biophys. J."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"014110","DOI":"10.1063\/1.3456985","volume":"133","author":"Bhatt D.","year":"2010","journal-title":"J. Chem. 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Chem."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"Pronk S.","year":"2013","journal-title":"Bioinformatics"},{"key":"ref51\/cit51","first-page":"1","volume":"117","author":"Plimpton S.","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0010-4655(99)00529-9","volume":"128","author":"Lyubartsev A. P.","year":"2000","journal-title":"Comput. Phys. Commun."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1002\/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O","volume":"18","author":"Procacci P.","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1002\/jcc.21388","volume":"31","author":"Marsili S.","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1002\/jcc.20303","volume":"26","author":"Christen M.","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"9725","DOI":"10.1021\/jp982255t","volume":"102","author":"Pappu R. V.","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"ref57\/cit57","first-page":"43","author":"Bowers K.","year":"2006","journal-title":"ACM\/IEEE Supercomputing."},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1098\/rsta.2004.1419","volume":"362","author":"Todorov I. T.","year":"2004","journal-title":"Philos. Trans. R. Soc., A"},{"key":"ref59\/cit59","first-page":"1","author":"Pronk S.","year":"2011","journal-title":"IEEE\/ACM Supercomputing"},{"key":"ref60\/cit60","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1021\/ct900620b","volume":"6","author":"Bowman G. R.","year":"2010","journal-title":"J. Chem. 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