Dynamical simulation methods quasi-harmonic dynamics

The idea of the Green s function/principal component analysis is closely related to the essential dynamics approach recently introduced into biomolecular simulations. Other similar works include those by Garcia, Ichiye and Karplus, Go and coworkers,and developers of the quasi-harmonic method. " The basic idea of the essential dynamics approach is to diagonalize a covariance matrix a whose elements are given by the formula... 

However, the drawback of ab initio calculations is that they usually refer to the athermal limit (T = 0 K), so that pressure but not temperature effects are included in the simulation. Although in principle the ab initio molecular dynamics approach[13] is able to overcome this limitation, at the present state of the art no temperature-dependent quantum-meehanieal simulations are feasible yet for mineral systems. Thus thermal properties have to be dealt with by methods based on empirical interatomic potential functions, containing parameters to be fitted to experimental quan-tities[14,15, 16]. The computational scheme applied here to carbonates is that based on the quasi-harmonic approximation for representing the atomic motion[17]. 

At low temperatures, if most of the anharmonic effects are due to lattice expansion, the quasi-harmonic approximation can be successfully applied. However, if the average displacement of the atoms is so large that the potential energy cannot be approximated by quadratic terms anymore, the approximation fails. In such cases, we can use a classical simulation method such as molecular dynamics to sample the phase space and calculate observables using these samples. We should note that this is strictly valid only in case of high temperatures, where Tmd Tqm-... 

Expression 11.3 provides the whole simulated spectrum, while a detailed vibrational analysis requires the unambiguous assignment of each mode contribution. Recently, a number of methods appeared in the literature aimed at the extraction of normal-mode-like analysis from ab initio dynamics [58-63]. Some of these [58-60] refer to the quasi-harmonic model introduced by Karplus [64,65] in the framework of classical molecular dynamics and individuate normal-mode directions as main components of the nuclear fluctuations in the NVE or NVT ensemble. The quasinormal model relies on the equipartition of the kinetic energy among normal modes thus problems arise when the simulation time required to obtain such a distribution is computationally too expensive, as is often the case for ab initio dynamics. Other approaches [61-63] carry out the time evolution analysis in the momenta subspace instead of the configurational space. In these approaches the basic consideration is that, at any temperature, generalized normal modes g, correspond to uncorrelated momenta such that [61]... 

Here, the nonrandom excitation of C2H4F is described by the dynamics of the F - - C2H4 bimolecular reaction. To simulate chemical activation, proper initial conditions must be chosen for the reactants and for their relative properties. The procedure for choosing initial conditions for the reactant s relative properties is given below in the discussion of bimolecular reactions. The quasi-classical method may be used to select initial conditions for molecular reactants. The energy for a symmetric-top polyatomic molecule in a specific vibrational-rotational state may be approximated by the harmonic oscilla-tor/rigid rotor model... 

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