Abstract
In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.
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Acknowledgments
D.P.T. is an Alberta Innovates Health Solutions Scientist and the Alberta Innovates Technology Futures Strategic Chair in (Bio)Molecular Simulation. Work in his group supported by grants from the Natural Sciences and Engineering Research Council of Canada and the Canadian Institutes of Health Research.
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Monticelli, L., Tieleman, D.P. (2013). Force Fields for Classical Molecular Dynamics. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_8
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DOI: https://doi.org/10.1007/978-1-62703-017-5_8
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