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J."},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s007750050291","volume":"4","author":"Martel P. J.","year":"1999","journal-title":"J. Biol. Inorg. Chem."},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1007\/s007750100287","volume":"7","author":"Teixeira V. H.","year":"2002","journal-title":"J. Biol. Inorg. Chem."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1016\/S0006-3495(04)74331-3","volume":"86","author":"Teixeira V. H.","year":"2004","journal-title":"Biophys. J."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"12586","DOI":"10.1021\/ja808463e","volume":"131","author":"Machuqueiro M.","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"9706","DOI":"10.1063\/1.1370959","volume":"114","author":"B\u00f6rjesson U.","year":"2001","journal-title":"J. Chem. Phys."},{"key":"ref18\/cit18","first-page":"47","volume":"8","author":"Mertz J. E.","year":"1994","journal-title":"Int. J. High Perform. Comput. Appl."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"13551","DOI":"10.1021\/jp037841n","volume":"108","author":"B\u00f6rjesson U.","year":"2004","journal-title":"J. Phys. Chem. B"},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"164112","DOI":"10.1063\/1.2731781","volume":"126","author":"Stern H. A.","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"051911","DOI":"10.1103\/PhysRevE.66.051911","volume":"66","author":"Walczak A. M.","year":"2002","journal-title":"Phys. Rev. E"},{"key":"ref22\/cit22","doi-asserted-by":"crossref","first-page":"021915","DOI":"10.1103\/PhysRevE.69.021915","volume":"69","author":"D\u0142ugosz M.","year":"2004","journal-title":"Phys. Rev. E"},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.chemphys.2004.03.031","volume":"302","author":"D\u0142ugosz M.","year":"2004","journal-title":"Chem. Phys."},{"key":"ref24\/cit24","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1002\/jcc.20139","volume":"25","author":"Mongan J.","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1529\/biophysj.105.061341","volume":"89","author":"Khandogin J.","year":"2005","journal-title":"Biophys. J."},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"9363","DOI":"10.1021\/bi060706r","volume":"45","author":"Khandogin J.","year":"2006","journal-title":"Biochemistry"},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"4184","DOI":"10.1063\/1.1497164","volume":"117","author":"Baptista A. M.","year":"2002","journal-title":"J. Chem. Phys."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"2927","DOI":"10.1021\/jp056456q","volume":"110","author":"Machuqueiro M.","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1529\/biophysj.106.092445","volume":"92","author":"Machuqueiro M.","year":"2007","journal-title":"Biophys. J."},{"key":"ref30\/cit30","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1002\/prot.21923","volume":"72","author":"Machuqueiro M.","year":"2008","journal-title":"Proteins: Struct. Funct. Bioinf."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","first-page":"15989","DOI":"10.1021\/jp902991u","volume":"113","author":"Campos S. R. R.","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"ref32\/cit32","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1002\/anie.199009921","volume":"29","author":"van Gunsteren W. F.","year":"1990","journal-title":"Angew. Chem., Int. 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Chem."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1002\/jcc.540110404","volume":"11","author":"Besler B. H.","year":"1990","journal-title":"J. Comput. Chem."},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1002\/jcc.540110311","volume":"11","author":"Breneman C. M.","year":"1990","journal-title":"J. Comput. Chem."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"10269","DOI":"10.1021\/j100142a004","volume":"97","author":"Bayly C. I.","year":"1993","journal-title":"J. Phys. Chem."},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1002\/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P","volume":"19","author":"Sigfridsson E.","year":"1998","journal-title":"J. Comput. Chem."},{"key":"ref42\/cit42","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1002\/jcc.20157","volume":"26","author":"Martin F.","year":"2005","journal-title":"J. Comput. 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D.","year":"1988","journal-title":"Phys. Rev. A"},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","volume":"37","author":"Lee C.","year":"1988","journal-title":"Phys. Rev. B"},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1139\/p80-159","volume":"58","author":"Vosko S. H.","year":"1980","journal-title":"Can. J. Phys"},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1021\/ct8000409","volume":"4","author":"Roy L. E.","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/BF00533485","volume":"28","author":"Hariharan P. C.","year":"1973","journal-title":"Theor. Chem. Acc."},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1063\/1.476673","volume":"109","author":"Rassolov V. A.","year":"1998","journal-title":"J. Chem. Phys."},{"key":"ref54\/cit54","doi-asserted-by":"crossref","first-page":"3654","DOI":"10.1063\/1.444267","volume":"77","author":"Francl M. M.","year":"1982","journal-title":"J. Chem. Phys."},{"key":"ref55\/cit55","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1006\/jmbi.1993.1620","volume":"234","author":"Matias P. M.","year":"1993","journal-title":"Mol. Biol."},{"key":"ref56\/cit56","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S0020-1693(97)06018-0","volume":"273","author":"Sim\u00f5es P.","year":"1998","journal-title":"Inorg. Chim. Acta"},{"key":"ref57\/cit57","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1021\/ci050400b","volume":"46","author":"Guha R.","year":"2006","journal-title":"J. Chem. Inf. Model"},{"key":"ref58\/cit58","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1021\/cr00046a002","volume":"81","author":"Scheidt W. R.","year":"1981","journal-title":"Chem. Rev."},{"key":"ref59\/cit59","doi-asserted-by":"crossref","first-page":"5003","DOI":"10.1021\/ja00169a002","volume":"112","author":"Gadsby P. M. A.","year":"1990","journal-title":"J. Am. Chem. Soc."},{"key":"ref60\/cit60","doi-asserted-by":"crossref","first-page":"12431","DOI":"10.1021\/bi981189i","volume":"37","author":"Ma J.-G.","year":"1998","journal-title":"Biochemistry"},{"key":"ref61\/cit61","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"Case D. A.","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref62\/cit62","doi-asserted-by":"crossref","first-page":"7821","DOI":"10.1039\/c0cp00111b","volume":"12","author":"Dupradeau F. Y.","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref63\/cit63","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/0022-2836(92)91009-E","volume":"224","author":"Bashford D.","year":"1992","journal-title":"J. Mol. Biol."},{"key":"ref64\/cit64","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","volume":"91","author":"Berendsen H. J. C.","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"ref65\/cit65","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"Lindahl E.","year":"2001","journal-title":"J. Mol. Model."},{"key":"ref66\/cit66","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1002\/bip.360230807","volume":"23","author":"Hermans J.","year":"1984","journal-title":"Biopolymers"},{"key":"ref67\/cit67","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"Hess B.","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref68\/cit68","doi-asserted-by":"crossref","first-page":"5451","DOI":"10.1063\/1.469273","volume":"102","author":"Tironi I. G.","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref69\/cit69","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"Berendsen H. J. C.","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref70\/cit70","volume-title":"The PyMOL User\u2019s Manual","author":"DeLano W. L.","year":"2002"},{"key":"ref71\/cit71","unstructured":"Zhurko, G. A.; Zhurko, D. A.Chemcraft: Graphical program for working with quantum chemistry computations, version 1.6. 2009."},{"key":"ref72\/cit72","unstructured":"Crawford, D.Gnuplot: An interactive plotting program, version 4.2. 2007."},{"key":"ref73\/cit73","volume-title":"Computer Simulation of Liquids","author":"Allen P. M.","year":"1997"},{"key":"ref74\/cit74","first-page":"1169","volume":"1767","author":"Paquete C. M.","year":"2007","journal-title":"Biochem. Biophys. Acta"},{"key":"ref75\/cit75","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1073\/pnas.54.6.1658","volume":"54","author":"Harbury H. 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