Cartesian coordinates general

Dirac showed in 1928 dial a fourth quantum number associated with intrinsic angidar momentum appears in a relativistic treatment of the free electron, it is customary to treat spin heiiristically. In general, the wavefimction of an electron is written as the product of the usual spatial part (which corresponds to a solution of the non-relativistic Sclnodinger equation and involves oidy the Cartesian coordinates of the particle) and a spin part a, where a is either a or p. A connnon shorthand notation is often used, whereby... 

To generalize what we have just done to reactive and inelastic scattering, one needs to calculate numerically integrated trajectories for motions in many degrees of freedom. This is most convenient to develop in space-fixed Cartesian coordinates. In this case, the classical equations of motion (Hamilton s equations) are given... 

Ciccotti G, Ferrario M and Ryckaert J-P 1982 Molecular dynamics of rigid systems in cartesian coordinates. A general formulation Mol. Phys. 47 1253-64... 

We tieat this case first, since it is simpler than the trigonal case. The molecular displacements are denoted by x and y (with suitable choice of their origins and of scaling). Then, without loss of generality we can denote the positions of the ci pairs in Cartesian coordinates by... 

Mathematical derivations presented in the following sections are, occasionally, given in the context of one- or two-dimensional Cartesian coordinate systems. These derivations can, however, be readily generalized and the adopted style is to make the explanations as simple as possible. 

Rate of Deformation Tensor For general three-dimensional flows, where all three velocity components may be important and may vaiy in all three coordinate directions, the concept of deformation previously introduced must be generahzed. The rate of deformation tensor Dy has nine components. In Cartesian coordinates. 

These difficulties have led to a revival of work on internal coordinate approaches, and to date several such techniques have been reported based on methods of rigid-body dynamics [8,19,34-37] and the Lagrange-Hamilton formalism [38-42]. These methods often have little in common in their analytical formulations, but they all may be reasonably referred to as internal coordinate molecular dynamics (ICMD) to underline their main distinction from conventional MD They all consider molecular motion in the space of generalized internal coordinates rather than in the usual Cartesian coordinate space. Their main goal is to compute long-duration macromolecular trajectories with acceptable accuracy but at a lower cost than Cartesian coordinate MD with bond length constraints. This task mrned out to be more complicated than it seemed initially. 

To obtain thermodynamic perturbation or integration formulas for changing q, one must go back and forth between expressions of the configuration integral in Cartesian coordinates and in suitably chosen generalized coordinates [51]. This introduces Jacobian factors... 

In the second step, the spatial restraints and the CHARMM22 force field tenns enforcing proper stereochemistry [80,81] are combined into an objective function. The general form of the objective function is similar to that in molecular dynamics programs such as CHARMM22 [80]. The objective function depends on the Cartesian coordinates of —10,000 atoms (3D points) that form a system (one or more molecules) ... 

The third quantum number m is called the magnetic quantum number for it is only in an applied magnetic field that it is possible to define a direction within the atom with respect to which the orbital can be directed. In general, the magnetic quantum number can take up 2/ + 1 values (i.e. 0, 1,. .., /) thus an s electron (which is spherically symmetrical and has zero orbital angular momentum) can have only one orientation, but a p electron can have three (frequently chosen to be the jc, y, and z directions in Cartesian coordinates). Likewise there are five possibilities for d orbitals and seven for f orbitals. 

Corresponding factors characterizing a general homogeneous deformation with reference to Cartesian coordinates. 

It is in general possible to find a Cartesian coordinate system attached to the molecule such that the tensor / takes a diagonal form. In terms of these so-called principal axes Equation (10) is simplified in that all cross terms are eliminated. Namely,... 

The general definition of a projection has been given on p. 23 in Eq. (2.37). For the purpose of illustration let us write down an example. If s = (Si,Sj,Sk) is a representation of the scattering vector in orthogonal Cartesian coordinates, then the aforementioned ID projection is... 

Fig. 2.5. Possible applications of a coupling parameter, A, in free energy calculations, (a) and (b) correspond, respectively, to simple and coupled modifications of torsional degrees of freedom, involved in the study of conformational equilibria (c) represents an intramolecular, end-to-end reaction coordinate that may be used, for instance, to model the folding of a short peptide (d) symbolizes the alteration of selected nonbonded interactions to estimate relative free energies, in the spirit of site-directed mutagenesis experiments (e) is a simple distance separating chemical species that can be employed in potential of mean force (PMF) calculations and (f) corresponds to the annihilation of selected nonbonded interactions for the estimation of e.g., free energies of solvation. In the examples (a), (b), and (e), the coupling parameter, A, is not independent of the Cartesian coordinates, x. Appropriate metric tensor correction should be considered through a relevant transformation into generalized coordinates...

The term J is the determinant of the Jacobian matrix upon changing from Cartesian to generalized coordinates. It measures the change in volume element between dxdp, and d polar coordinate J = r and therefore dxdy = r dr <17. The derivative of A is therefore the sum of two contributions the mechanical forces acting along (dU/<9 ), and the change of volume element. The term -1//3 d In J /<9 is effectively an entropic contribution. 

This Hamiltonian is distinct from jg since it is a function of (x p.j (set of Cartesian coordinates) whereas jgf is a function of (q, p,) (generalized coordinates). 

Equation A.7 represents conservation of mass for a general flow in rectangular Cartesian coordinates. 

The matrix to be diagonalized for finding the vibrational frequencies is the matrix product of the above G matrix for Cartesian coordinates and the corresponding F matrix for Cartesian displacement coordinates. It is noted in passing that the GF matrix is generally not symmetric, i.e. 

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