Metric tensor corrections

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...

Al) Freezing of bonds and angles defonns the phase space of the molecule and perturbs the time averages. The MD results, therefore, require a complicated correction with the so-called metric tensor, which undermines any gain in efficiency due to elimination of variables [10,17-20]. 

Bl) The metrics effect is very significant in special theoretical examples, like a freely joined chain. In simulations of polymer solutions of alkanes, however, it only slightly affects the static ensemble properties even at high temperatures [21]. Its possible role in common biological applications of MD has not yet been studied. With the recently developed fast recursive algorithms for computing the metric tensor [22], such corrections became affordable, and comparative calculations will probably appear in the near future. 

Equations (6.4) describe the balance between two unknowns - the fundamental tensor and the distribution of matter in a system of interest. Although the distribution function is not conditioned by the theory of relativity in any way, it assumes critical importance in deciding the appropriate space-time geometry in cosmological applications. This way the metric tensor is defined, not on the basis of relativistic considerations, but on Newtonian principles. Cosmological models arrived at in this way we consider non-relativistic, unless the metric tensor has the correct relativistic signature. To explain the reasoning we consider a few elementary models. 

Atomic basis functions in quantum chemistry transform like covariant tensors. Matrices of molecular integrals are therefore fully covariant tensors e.g., the matrix elements of the Fock matrix are F v = (Xn F Xv)- In contrast, the density matrix is a fully contravariant tensor, P = (x IpIx )- This representation is called the covariant integral representation. The derivation of working equations in AO-based quantum chemistry can therefore be divided into two steps (1) formulation of the basic equations in natural tensor representation, and (2) conversion to covariant integral representation by applying the metric tensors. The first step yields equations that are similar to the underlying operator or orthonormal-basis equations and are therefore simple to derive. The second step automatically yields tensorially correct equations for nonorthogonal basis functions, whose derivation may become unwieldy without tensor notation because of the frequent occurrence of the overlap matrix and its inverse. 

Although the metric g has been defined as constant by Eq. (3.8), we have just shown that it perfectly fits into the definition of a tensor and features the correct transformation property under Lorentz transformations. Another very useful fourth-rank Lorentz tensor is the totally antisymmetric Levi-Civit (pseudo-)tensor whose contravariant components are defined by... 

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