Molecular dynamics definition

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics 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. 

To make evaluations more definite, we use optical and microwave experimental data, as well as calculations of molecular dynamics of certain simple liquids which usually fit the experiment. Rotation is everywhere considered as classical, and the objects are two-atomic and spherical molecules, as well as hard ellipsoids. 

Recent molecular dynamics studies of properties of the water surface have led to predictions of the surface potential of water that differ not only in magnitude but also in sign. The main problem is connected with the difficulty of proper definition of the surface potential of a real polar... 

Also note that the definition of the effective potential V in (8.14) enables one to conceive a constant-temperature molecular dynamics method (instead of MC) to generate the Tsallis distributions. Given this effective potential, it is possible to define a constant-temperature molecular dynamics algorithm such that the distribution Pq(x) is sampled in the trajectory. The equation of motion takes on the simple and suggestive form... 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

Within the mixed quantum/classical approach, at each time step in a classical molecular dynamics simulation (that is, for each configuration of the bath coordinates), for each chromophore one needs the transition frequency and the transition dipole or polarizability, and if there are multiple chromophores, one needs the coupling frequencies between each pair. For water a number of different possible approaches have been used to obtain these quantities in this section we begin with brief discussions of each approach to determine transition frequencies. For definiteness we consider the case of a single OH stretch chromophore on an HOD molecule in liquid D2O. 

None of the methods currently used to study molecular dynamics can span the whole time range of motions of interest, from picoseconds to seconds and minutes. However, the structural resolution of a method is of equal importance. A method has to not only provide information about the existence of motions with definite velocities but also to identify what structural element is moving and what is the mechanism of motion. Computer simulation of molecular dynamics has proved to be a very important tool for the development of theories concerning times and mechanisms of motions in proteins. In this approach, the initial coordinates and forces on each atom are input into the calculations, and classical equations of motions are solved by numerical means. The lengthy duration of the calculation procedure, even with powerful modem computers, does not permit the time interval investigated to be extended beyond hundreds of picoseconds. In addition, there are strong... 

Abstract The theoretical basis for the quantum time evolution of path integral centroid variables is described, as weU as the motivation for using these variables to study condensed phase quantum dynamics. The equihbrium centroid distribution is shown to be a well-defined distribution function in the canonical ensemble. A quantum mechanical quasi-density operator (QDO) can then be associated with each value of the distribution so that, upon the application of rigorous quantum mechanics, it can be used to provide an exact definition of both static and dynamical centroid variables. Various properties of the dynamical centroid variables can thus be defined and explored. Importantly, this perspective shows that the centroid constraint on the imaginary time paths introduces a non-stationarity in the equihbrium ensemble. This, in turn, can be proven to yield information on the correlations of spontaneous dynamical fluctuations. This exact formalism also leads to a derivation of Centroid Molecular Dynamics, as well as the basis for systematic improvements of that theory. 

The most definitive proof of p-sheet structure requires the determination of the three-dimensional solution structure of the peptide. For the calculation of such structures one requires the accurate determination of coupling constants by DQF-COSY experiments which give backbone dihedral restraints and through-space connectivities (ROESY or NOESY experiments) which give rise to distance restraints. A combination of these restraints allows the calculation of the three-dimensional structure of the peptide using restrained molecular dynamics simulations. Utilizing this methodology, the three-dimensional structures of a number of cyclic peptides have been solved.[411... 

The solution structures of a number of metalloproteins with paramagnetic metal centers were determined with molecular mechanics and dynamics in combination with NMR spectroscopy (see also Chapter 9)1124-126,189]. Due to the complexity of the molecules, for metalloproteins a crystal structure of the compound or a derivative is often needed for the definition of the starting geometry. Molecular dynamics is then used to find low-eneigy conformers. The dynamics calculations also allow the visualization of areas of large flexibility, and this may lead to some understanding of the enzyme mechanism11891. 

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