Free energy reaction root mapping of alanine tripeptide in water

References

• K. Fukui, Acc. Chem. Res. 14 (12), 363–368 (1981).
   Web of Science ®Google Scholar
• K. Fukui, Int. J. Quantum Chem. 20 (S15), 633–642 (1981).
   Google Scholar
• Y. Zhang, H. Liu, and W. Yang, J. Chem. Phys. 112 (8), 3483–3492 (2000).
   Web of Science ®Google Scholar
• B. Ensing, A. Laio, F.L. Gervasio, M. Parrinello, and M.L. Klein, J. Am. Chem. Soc. 126 (31), 9492–9493 (2004).
   PubMed Web of Science ®Google Scholar
• P. Fleurat-Lessard and T. Ziegler, J. Chem. Phys. 123, 084101 (2005).
   PubMed Web of Science ®Google Scholar
• L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006).
   PubMed Web of Science ®Google Scholar
• I.V. Khavrutskii, K. Arora, and C.L. Brooks, J. Chem. Phys. 125 17, (2006).
   PubMedGoogle Scholar
• H. Hu, Z. Lu, and W. Yang, J. Chem. Theory Comput. 3 (2), 390–406 (2007).
   PubMed Web of Science ®Google Scholar
• L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 446 (1–3), 182–190 (2007).
   Web of Science ®Google Scholar
• H. Hu, Z. Lu, J.M. Parks, S.K. Burger, and W. Yang, J. Chem. Phys. 128, 034105 (2008).
   PubMed Web of Science ®Google Scholar
• J.G. Kirkwood, J. Chem. Phys. 3 (5), 300–313 (1935).
   Google Scholar
• E.A. Carter, G. Ciccotti, J.T. Hynes, and R. Kapral, Chem. Phys. Lett. 156 (5), 472–477 (1989).
   Web of Science ®Google Scholar
• T.P. Straatsma, H.J.C. Berendsen, and J.P.M. Postma, J. Chem. Phys. 85 (11), 6720–6727 (1986).
   Web of Science ®Google Scholar
• D.L. Beveridge and F.M. Dicapua, Annu. Rev. Biophys. Biophys. Chem. 18, 431–492 (1989).
   PubMedGoogle Scholar
• J. Hermans, J. Phys. Chem. 95 (23), 9029–9032 (1991).
   Web of Science ®Google Scholar
• H. Grubmüller, B. Heymann, and P. Tavan, Science. 271, 997–999 (1996).
   PubMed Web of Science ®Google Scholar
• S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten, Biophys. J. 72 (4), 1568–1581 (1997).
   PubMed Web of Science ®Google Scholar
• M. Balsera, S. Stepaniants, S. Izrailev, Y. Oono, and K. Schulten, Biophys. J. 73 (3), 1281–1287 (1997).
   PubMed Web of Science ®Google Scholar
• E. Evans and K. Ritchie, Biophys. J. 72 (4), 1541–1555 (1997).
   PubMed Web of Science ®Google Scholar
• A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. 99 (20), 12562–12566 (2002).
   PubMed Web of Science ®Google Scholar
• A. Barducci, M. Bonomi, and M. Parrinello, Wiley Interdiscip. Rev. Comput. Mol. Sci. 1 (5), 826–843 (2011).
   Web of Science ®Google Scholar
• L. Sutto, S. Marsili, and F.L. Gervasio, Wiley Interdiscip. Rev. Comput. Mol. Sci. 2 (5), 771–779 (2012).
   Web of Science ®Google Scholar
• G.M. Torrie and J.P. Valleau, Chem. Phys. Lett. 28 (4), 578–581 (1974).
   Web of Science ®Google Scholar
• G.M. Torrie and J.P. Valleau, J. Comput. Phys. 23 (2), 187–199 (1977).
   Web of Science ®Google Scholar
• P. Maragakis, A. Van Der Vaart, and M. Karplus, J. Phys. Chem. B. 113 (14), 4664–4673 (2009).
   PubMed Web of Science ®Google Scholar
• M. Chen, T.-Q. Yu, and M.E. Tuckerman, Proc. Natl. Acad. Sci. U.S.A. 112 (11), 3235–3240 (2015).
   PubMed Web of Science ®Google Scholar
• M. Chen, M. a Cuendet, and M.E. Tuckerman, J. Chem. Phys. 137 (2), 024102 (2012).
   PubMedGoogle Scholar
• A.K. Tummanapelli and S. Vasudevan, J. Phys. Chem. B. 119 (49), 15353–15358 (2015).
   PubMed Web of Science ®Google Scholar
• E.M. Boczko and C.L. Brooks, J. Phys. Chem. 97 (17), 4509–4513 (1993).
   Web of Science ®Google Scholar
• Y. Mitsuta, S. Yamanaka, T. Kawakami, and M. Okumura, J. Comput. Chem. 39 (23), 1913–1912 (2018).
   PubMed Web of Science ®Google Scholar
• J. Kästner and W. Thiel, J. Chem. Phys. 124 (23), 234106 (2006).
   PubMedGoogle Scholar
• K. Ohno and S. Maeda, Chem. Phys. Lett. 384 (4–6), 277–282 (2004).
   Web of Science ®Google Scholar
• S. Maeda and K. Ohno, J. Phys. Chem. A. 109 (25), 5742–5753 (2005).
   PubMed Web of Science ®Google Scholar
• K. Ohno and S. Maeda, J. Phys. Chem. A. 110 (28), 8933–8941 (2006).
   PubMed Web of Science ®Google Scholar
• J. Kästner, J. Chem. Phys. 131 (3), 034109 (2009).
   PubMedGoogle Scholar
• M.U. Bohner and J. Kästner, J. Chem. Phys. 137 (3), 0–6 (2012).
   PubMedGoogle Scholar
• J. Nocedal, Math. Comput. 35 (151), 773–773 (1980).
   Web of Science ®Google Scholar
• P. Pulay and G. Fogarasi, J. Chem. Phys. 96 (4), 2856–2860 (1992).
   Web of Science ®Google Scholar
• Y. Mitsuta, T. Kawakami, M. Okumura, and S. Yamanaka, Int. J. Mol. Sci. 19, 937 (2018).
   Google Scholar
• S. Kumar, J.M. Rosenberg, D. Bouzida, R.H. Swendsen, and P.A. Kollman, J. Comput. Chem. 16 (11), 1339–1350 (1995).
   Web of Science ®Google Scholar
• J. Kästner, Wiley Interdiscip. Rev. Comput. Mol. Sci. 1 (6), 932–942 (2011).
   Web of Science ®Google Scholar
• T. Hastie, R. Tibshirani, and J. Friedman, Bayesian Forecast. Dyn. Model. 1, 1–694 (2009).
   Google Scholar
• Y. Luo, S. Maeda, and K. Ohno, J. Phys. Chem. A. 111, 10732–10737 (2007).
   PubMedGoogle Scholar
• J. Baker, J. Comput. Chem. 7 (4), 385–395 (1986).
   Web of Science ®Google Scholar
• G. Henkelman and H. Jónsson, J. Chem. Phys. 111 (15), 7010–7022 (1999).
   Web of Science ®Google Scholar
• A. Heyden, A.T. Bell, and F.J. Keil, J. Chem. Phys. 123 (22), 224101 (2005).
   PubMed Web of Science ®Google Scholar
• J. Kästner and P. Sherwood, J. Chem. Phys. 128 (1), 014106 (2008).
   PubMedGoogle Scholar
• A. Liljas, L. Liljas, J. Pisku, G. Lindblom, P. Nissen, and M. Kjeldgaard, Textbook of Structural Biology (World Scientific Publishing, Singapore, 2009).
   Google Scholar
• N. Foloppe and A.D. MacKerell, Jr., J. Comput. Chem. 21 (2), 86–104 (2000).
   Web of Science ®Google Scholar
• W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, J. Chem. Phys. 79 (2), 926–935 (1983).
   Web of Science ®Google Scholar
• G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126, 014101 (2007).
   PubMed Web of Science ®Google Scholar
• M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids (Oxford Science Publications, New York, 1987).
   Google Scholar
• M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, SoftwareX. 1–2, 19–25 (2015).
   Google Scholar
• G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, and G. Bussi, Comput. Phys. Commun. 185 (2), 604–613 (2014).
   Web of Science ®Google Scholar
• H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, Nucleic Acids Res. 28 (1), 235–242 (2000).
   PubMed Web of Science ®Google Scholar
• M. Novotny and G.J. Kleywegt, J. Mol. Biol. 347 (2), 231–241 (2005).
   PubMed Web of Science ®Google Scholar
• N. Nakajima, J. Higo, and A. Kidera, J. Mol. Biol. 296, 197–216 (2000).
   PubMed Web of Science ®Google Scholar