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References
van Gunsteren, W.F. and Berendsen, H.J.C. (1987) Groningen Molecular Simulation (GROMOS) Library Manual. Biomos, Groningen.
Weiner, P.K. and Kollman, P.A. (1981) AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2, 287–303.
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. (1983) A program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4, 187–217.
Jorgensen, W.L. and Tirado-Rives, J. (1988) The OPLS potential functions for proteins. energy minimizations for crystals of cyclic peptides and Crambin. J. Am. Chem. Soc. 110, 1657–1666.
Jorgensen, W.L., Maxwell, D.S., and Tirado-Rives, J. (1996) Development and testing of the OPLS All-Atom Force Field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225–11236.
Berman, H.M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235–242.
Lovas, S. and Murphy, R.F. (1997) Molecular modeling of neuropeptides. Methods Mol. Biol. 73, 209–217.
Oostenbrink, C., Villa, A., Mark, A.E., and van Gunsteren, W.F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS forcefield parameter sets 53A5 and 53A6. J. Comput. Chem. 13,1656–1676.
Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. (1997) LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472.
Berendsen, H.J.C., Postma, J.P.M., DiNola, A., and Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690.
van der Spoel, D., Lindahl, E., Hess, B., et al. (2005) Gromacs User Manual version 3.3, www.gromacs.org.
Sugita, Y. and Okamoto, Y. (1999) Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141–151.
Baumketner, A. and Shea, J.-E. (2005) Free energy landscapes for amyloidogenic tetrapeptides dimerization. Biophys. J. 89, 1493–1503.
Nguyen, P.H., Mu, Y., and Stock, G. (2005) Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins 60, 485–494.
Seibert, M.M., Patriksson, A., Hess, B., and van der Spoel, D. (2005) Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354, 173.
www.gromacs.org/pipermail/gmx-revision/2006-August/000152.html
van der Spoel, D. and van Maaren, P.J. (2006) The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theor. Comp. 2, 1–11.
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092.
Essman, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., and Pedersen, L.G. (1995) A smooth particle mesh ewald potential. J. Chem. Phys. 103,8577–8592.
Tironi, I.G., Sperb, R., Smith, P.E., and van Gunsteren, W.F. (1995) A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102,5451–5459.
Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341.
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Copps, J., Murphy, R.F., Lovas, S. (2008). Molecular Dynamics Simulations of Peptides. In: Otvos, L. (eds) Peptide-Based Drug Design. Methods In Molecular Biology™, vol 494. Humana Press. https://doi.org/10.1007/978-1-59745-419-3_7
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DOI: https://doi.org/10.1007/978-1-59745-419-3_7
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