Molecular dynamics initial condition selection

Besides its practical importance, photodissociation — especially of small polyatomic molecules — provides an ideal opportunity for the study of molecular dynamics on a detailed state-to-state level. We associate with molecular dynamics processes such as energy transfer between the various molecular modes, the breaking of chemical bonds and the creation of new ones, transitions between different electronic states etc. One goal of modern physical chemistry is the microscopical understanding of molecular reactivity beyond purely kinetic descriptions (Levine and Bernstein 1987). Because the initial conditions can be well defined (absorption of a single monochromatic photon, preparation of the parent molecule in selected quantum states), photodissociation is ideally suited to address questions which are unprecedented in chemistry. The last decade has witnessed an explosion of new experimental techniques which nowadays makes it possible to tackle questions which before were beyond any practical realization (Ashfold and Baggott 1987). 

The remaining aspect of a trajectory simulation is choosing the initial momenta and coordinates. These initial conditions are chosen so that the results from an ensemble of trajectories may be compared with experiment and/or theory, and used to make predictions about the chemical system s molecular dynamics. In this chapter Monte Carlo methods are described for sampling the appropriate distributions for initial values of the coordinates and momenta. Trajectories may be integrated in different coordinates and conjugate momenta, such as internal [7], Jacobi [8], and Cartesian. However, the Cartesian coordinate representation is most general for systems of any size and the Monte Carlo selection of Cartesian coordinates and momenta is described here for a variety of chemical processes. Many of... 

In its simplest sense classical molecular dynamics involves integrating the classical equations of motion for a set of molecules. In this regard, the most salient issues concern initial simulation conditions, numeric integration of the equations of motion, ensembles selection, equilibration, and checks on the simulation. 

In some molecular dynamics work, the process of equilibration has accounted for a substantial fraction of the total computer time devoted to the calculation. If the intermolecular potential has a sufficiently short range, however, it is possible to use only a fraction of the molecular dynamics system for equilibration. One can set aside a subsystem containing, say, an eighth of the total number of molecules, select initial conditions, and allow the... 

Execution of the method requires the physical domain to be divided into a distribution of conqiutational cells. The cells provide geometric boundaries and volumes, which are used to sample macroscopic properties. Also, only molecules located within the same cell, at a given time, are allowed to collide. The DSMC simulation proceeds from a set of prescribed initial condition. The molecules randomly populate the computational domain. These simulated molecules are assigned random velocities, usually based on the equilibrium distribution. The simulated representative particles move for a certain time step. This molecule motion is modeled deterministically. This process enforces the boundary conditions. With the simulated particles being appropriately indexed, the molecular collision process can be performed. The collision process is modeled statistically, which is different from deterministic simulation methods such as the molecular dynamics methods. In general, only particles within the same computational cell are considered to be possible collision partners. Mthin each cell, collision pairs are selected randomly and a representative set of collisions is performed. The post-collision velocities are determined. There are several... 

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... 

The initial conditions for the vibrational modes of the (gly-FI)+ were chosen via the quasiclassical normal-mode method, with the energy for each normal mode of vibration selected from the mode s 300 K harmonic oscillator Boltzmann distribution. A 300 K rotational energy of RT/2 was added to each principal axis of rotation of the projectile. Initial conditions for the diamond surface were chosen by first equiHbrating the surface to a 300 K Boltzmann distribution with 2 ps of molecular dynamics and scaHng the atomic velocities. The structure and atomic velocities obtained from this equilibration process are then used as the initial conditions for an equilibration run at the beginning of each trajectory. 

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