Dipoles molecular system simulations

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

Fig. 4.1 a Typical time evolution of a given correlation function in a glass-forming system for different temperatures (T >T2>...>T ), b Molecular dynamics simulation results [105] for the time decay of different correlation functions in polyisoprene at 363 K normalized dynamic structure factor at the first static structure factor maximum solid thick line)y intermediate incoherent scattering function of the hydrogens solid thin line), dipole-dipole correlation function dashed line) and second order orientational correlation function of three different C-H bonds measurable by NMR dashed-dotted lines)... 

Simulations of charged systems are very important. Common examples are plasmas, ionic solutions, dipole system and electronic systems. Because all pairs are included in the sum of eq. (2), the computer time only depends on the number of atoms and the number of time steps. For this reason my results should be applicable to all similar systems. I will discuss here only results for molecular dynamics simulations. The situation for Monte Carlo is completely parallel, although the actual coding is different since atoms are moved singly rather than all together. 

Other Work on Water-Related Systems. Sonoda et al.61 have simulated a time-resolved optical Kerr effect experiment. In this model, which uses molecular dynamics to represent the behaviour of the extended medium, the principle intermolecular effects are generated by the dipole-induced-dipole (DID) mechanism, but the effect of the second order molecular response is also include through terms involving the static molecular / tensor, calculated by an MP2 method. Weber et al.6S have applied ab initio linear scaling response theory to water clusters. Skaf and Vechi69 have used MP2/6-311 ++ G(d,p) calculation of the a and y tensors of water and dimethylsulfoxide (DMSO) to carry out a molecular dynamics simulation of DMSO/Water mixtures. Frediani et al.70 have used a new development of the polarizable continuum model to study the polarizability of halides at the water/air interface. 

For periodically replicated nonconducting molecular systems, the complex dielectric permittivity s(co) can be computed from the time autocorrelation function (ACF) of the total dipole moment [64] during the course of a simulation run as follows ... 

The potential parameters for the water molecule were empirically fitted to reproduce the experimental dipole moment, 0-H bond length and H-O-H angle of the water monomer and the structure of the water dimer and infra-red data. Molecular dynamics simulations were then used to calculate the self-diffusion coefficient, radial distribution functions (RDFs) and energy of evaporation of liquid water. The computer code DL POLY 2.6 code (Forester and Smith 1995) was employed. We simulated a box containing 256 water molecules at a temperature of 300 K where the conditions were initially set at the experimental density of p= 1.0 g/cm and run with an NPT ensemble. We chose a mass for the oxygen shell of 0.2 a.u., which is small compared to the mass of the hydrogen atom of 1.0 a.u. However, due to the small shell mass we needed to run the MD simulation with the small timestep of 0.2 fs in order to keep the system stable. With this timestep we obtained data at constant pressure and temperature for a period of 100 picoseconds. 

Very recently in work not yet published (15). Hassis-Bezot. Bossis. and Brot have done 3-D molecular dynamics simulations of a system of dipolar molecules interacting with a Stockmayer pair potential (Lennard-Jones plus point dipole-dipole coupling), with 913 and 1472 molecules in a spherical dish potential of the sort just described. Computer runs were done at reduced density p = o.g, temperature T =... 

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