Molecular Dynamics with Polarizable Force Fields

As electric fields and potential of molecules can be generated upon distributed p, the second order energies schemes of the SIBFA approach can be directly fueled by the density fitted coefficients. To conclude, an important asset of the GEM approach is the possibility of generating a general framework to perform Periodic Boundary Conditions (PBC) simulations. Indeed, such process can be used for second generation APMM such as SIBFA since PBC methodology has been shown to be a key issue in polarizable molecular dynamics with the efficient PBC implementation [60] of the multipole based AMOEBA force field [61]. 

MOLECULAR DYNAMICS WITH POLARIZABLE FORCE FIELDS... 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

Babin, V., Baucom, J., Darden, T. A., Sagui, C. (2006). Molecular dynamics simulations of DNA with polarizable force fields Convergence of an... 

NMR spectroscopy is a very useful tool for determining the local chemical surroundings of various atoms. Komin et al studied theoretically this for the adenine molecule of Fig. 20 both in vacuum and in an aqueous solution using different computational approaches. In all cases, density-functional calculations were used for the adenine molecule, but as basis functions they used either a set of localized functions (marked loc in Table 45) or plane waves (marked pw). Furthermore, in order to include the effects of the solvent they used either the polarizable continuum approach (marked PCM) or an explicit QM/MM model with a force field for the solvent and a molecular-dynamics approach for optimizing the structure (marked MD). In that case, the chemical shifts were calculated as averages over 40 snapshots from the molecular-dynamics simulations. Finally, in one case, an extra external potential from the solvent acting on the solute was included, too, marked by the asterisk in the table. 

The utility of CP dynamics is that it allows one to follow the electronic structure throughout the course of the simulation. This is not the case when empirical force fields are used. One simple property that can be evaluated throughout the CP liquid water simulation is the average dipole moment of a water molecule. The value extracted from these simulations, 2.66 D, is in good agreement with their cited experimental value of 2.6 Within CP dynamics, polarization of the water molecules (their gas phase dipole moment is 1.85 D) is automatically achieved, bypassing the parameterization process that use of a polarizable, nonadditive force field would entail. The ab initio molecular dynamics simulation also allowed them to follow the nature the lowest unoccupied molecular orbital (LUMO) which plays a role in the conduction of an excess electron. 

The choice of the adjustable parameters used in conjunction with classical potentials can result to either effective potentials that implicitly include the nuclear quantization and can therefore be used in conjunction with classical simulations (albeit only for the conditions they were parameterized for) or transferable ones that attempt to best approximate the Born-Oppenheimer PES and should be used in nuclear quantum statistical simulations. Representative examples of effective force fields for water consist of TIP4P (Jorgensen et al. 1983), SPC/E (Berendsen et al. 1987) (pair-wise additive), and Dang-Chang (DC) (Dang and Chang 1997) (polarizable, many-body). The polarizable potentials contain - in addition to the pairwise additive term - a classical induction (polarization) term that explicitly (albeit approximately) accounts for many-body effects to infinite order. These effective potentials are fitted to reproduce bulk-phase experimental data (i.e., the enthalpy at T = 298 K and the radial distribution functions at ambient conditions) in classical molecular dynamics simulations of liquid water. Despite their simplicity, these models describe some experimental properties of liquid... 

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