Trajectory calculations water cluster

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. 

Trajectory calculations for proton transfer and ionization in water cluster,112 116 isomerization,117 and various types of unimolecular reactions6,118 128 have been carried out, and the analyses on time course of the reaction, product ratio, and product energy distribution were reported. 

The protein-solvent interface was studied in an explicit solvent environment of 3182 water molecules by MD simulations performed on metmyoglobin [31].Both the structure and dynamics of the hydrated surface of myoglobin are similar to that obtained by experimental methods calculating three-dimensional density distributions, temperature factors and occupancy weights of the solvent molecules. On the basis of trajectories they identified multiple solvation layers around the protein surface including more than 500 hydration sites. Properties of theoretically calculated hydration clusters were compared to that obtained from neutron and X-ray data. This study indicates that the simulation unified the hydration picture provided by X-ray and neutron diffraction experiments. 

For the description of a solution of alanine in water two models were compared and combined with one another (79), namely the continuum model approach and the cluster ansatz approach (148,149). In the cluster approach snapshots along a trajectory are harvested and subsequent quantum chemical analysis is carried out. In order to learn more about the structure and the effects of the solvent shell, the molecular dipole moments were computed. To harvest a trajectory and for comparison AIMD (here CPMD) simulations were carried out (79). The calculations contained one alanine molecule dissolved in 60 water molecules. The average dipole moments for alanine and water were derived by means of maximally localized Wannier functions (MLWF) (67-72). For the water molecules different solvent shells were selected according to the three radial pair distributions between water and the functional groups. An overview about the findings is given in Tables II and III. 

The extended simple point charge (SPC/E) model [59] is used. This model is known to give reasonably accurate values of static dielectric permittivity of liquid water at ambient conditions [60]. The MD simulations were performed for both H2O and D2O with the system size of 1024 particles at 220 K, 240 K, 267 K, 273 K, 300 K, and 355 K. The parallel molecular dynamics code for arbitrary molecular mixtures (DynaMix) is implemented by Lyubartsev and Laaksonen [61]. The simulations have been carried out on a Linux cluster built on the Tyan/Opteron 64 platform, which enables calculations of relatively long trajectories for a system of 1024 water molecules. The simulation run lengths depend on temperature and are in the range between 1 ns and 4 ns for the warmest and coldest simulation, respectively. As the initial condition was a cubic lattice, the equilibration time was chosen to be temperature dependent in the range from 200 ps at 355 Ktol ns at 200K. 

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