Molecular dynamics (MD) simulations have been broadly applied to a wide variety of problems in which detailed intermolecular interactions impact equilibrium structures and structural dynamics. The utility of these simulations relies on well-developed force field parameters. In this talk results are presented for two different parameterization problems. One is, to our knowledge, the first modular parameterization of fluorescent protein chromophores, in which we have developed parameters for six commonly-used fluorescent proteins: EGFP, mCherry, DsRed, EBFP, EYFP, and ECFP. These parameters are consistent with current AMBER force fields—ff14SB (Maier et al. J. Chem. Theory Comput., 2015, 11, 3696-3713) and GAFF (Wang et al., J. Comput. Chem., 2004, 25, 1157-1174)—and can easily be extended to other fluorescent proteins. The other provides parameters for monovalent ions for use with the recently-developed Optimal Point Charge (OPC) water model (Izadi et al. J. Phys. Chem. Lett., 2014, 5, 3863-3871). Ion parameters are not generally transferable from one water model to another, so while the OPC model promises improved explicit solvent performance, it is of limited value without specifically designed ion parameters. We present extensive convergence testing as well as Lennard-Jones parameters for six monovalent ions for use with the OPC water model.

Two tales of molecular dynamics parameters: Fluorescent protein chromophores and aqueous ions

251st National Meeting (2016)

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