Born Oppenheimer approximation simulation potential

The applicability of the Born-Oppenheimer approximation for complex molecular systems is basic to all classical simulation methods. It enables the formulation of an effective potential field for nuclei on the basis of the SchrdJdinger equation. In practice this is not simple, since the number of electrons is usually large and the extent of configuration space is too vast to allow accurate initio determination of the effective fields. One has to resort to simplifications and semi-empirical or empirical adjustments of potential fields, thus introducing interdependence of parameters that tend to obscure the pure significance of each term. This applies in... 

We wanted to extend this approach to include dynamical effects on line shapes. As discussed earlier, for this approach one needs a trajectory co t) for the transition frequency for a single chromophore. One could extract a water cluster around the HOD molecule at every time step in an MD simulation and then perform an ab initio calculation, but this would entail millions of such calculations, which is not feasible. Within the Born Oppenheimer approximation the OH stretch potential is a functional of the nuclear coordinates of all the bath atoms, as is the OH transition frequency. Of course we do not know the functional. Suppose that the transition frequency is (approximately) a function of a one or more collective coordinates of these nuclear positions. A priori we do not know which collective coordinates to choose, or what the function is. We explored several such possibilities, and one collective coordinate that worked reasonably well was simply the electric field from all the bath atoms (assuming the point charges as assigned in the simulation potential) on the H atom of the HOD molecule, in the direction of the OH bond. 

In classical MD simulations it is often assumed that the nuclei move on a potential energy surface. Implicit in this assumption is that the Born-Oppenheimer approximation applies that electronic and nuclear motion can... 

As most of the electronic structure simulation methods, we start with the Born-Oppenheimer approximation to decouple the ionic and electronic degrees of freedom. The ions are treated classically, while the electrons are described by quantum mechanics. The electronic wavefunctions are solved in the instantaneous potential created by the ions, and are assumed to evolve adiabatically during the ionic dynamics, so as to remain on the Born-Oppenheimer surface. Beyond this, the most basic approximations of the method concern the treatment of exchange and correlation (XC) and the use of pseudopotentials. XC is treated within Kohn-Sham DFT [3]. Both the local (spin) density approximation (LDA/LSDA) [16] and the generalized gradients approximation (GGA) [17] are implemented. The pseudopotentials are standard norm-conserving [18, 19], treated in the fully non-local form proposed by Kleinman and Bylander [20]. 

Born-Oppenheimer approximation. In particular, they analyzed the time evolution of the ionization potential and the dependence of the dynamics on the initial temperature of the Aga molecule. The simulations were performed by use of the Verlet algorithm in its velocity form. 

Combining a microscopic electronic theory with molecular dynamics simulations in the Born-Oppenheimer approximation, Bennemann, Garcia, and Jeschke presented the first theoretical results for the ultrafast structural changes in the silver trimer [135]. They determined the timescale for the relaxation from the linear to a triangular structure initiated by a photodetachment process and showed that the time-dependent change of the ionization potential (IP) reflects in detail the internal degrees of freedom. 

The success of any molecular simulation method relies on the potential energy function for the system of interest, also known as force fields [27]. In case of proteins, several (semi)empirical atomistic force fields have been developed over the years, of which ENCAD [28,29], AMBER [30], CHARMM [31], GRO-MOS [32], and OPLSAA [33] are the most well known. In principle, the force field should include the electronic structure, but for most except the smallest systems the calculation of the electronic structure is prohibitively expensive, even when using approximations such as density functional theory. Instead, most potential energy functions are (semi)empirical classical approximations of the Born-Oppenheimer energy surface. 

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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