Internal coordinate molecular dynamics

IV. INTERNAL COORDINATE MOLECULAR DYNAMICS A. Main Problems and Historical Perspective... 

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. 

The full dynamical treatment of electrons and nuclei together in a laboratory system of coordinates is computationally intensive and difficult. However, the availability of multiprocessor computers and detailed attention to the development of efficient software, such as ENDyne, which can be maintained and debugged continually when new features are added, make END a viable alternative among methods for the study of molecular processes. Eurthemiore, when the application of END is compared to the total effort of accurate determination of relevant potential energy surfaces and nonadiabatic coupling terms, faithful analytical fitting and interpolation of the common pointwise representation of surfaces and coupling terms, and the solution of the coupled dynamical equations in a suitable internal coordinates, the computational effort of END is competitive. 

The internal architecture of HyperChem back ends is different from that expected to be used by third-party packages. To a third-party agent wishing to interface with HyperChem, HyperChem always acts as a server. Thus a third-party molecular dynamics package would ask HyperChem to send the coordinates of a molecule rather than HyperChem determining on its own that it should send coordinates at the appropriate time. 

Lipkowitz and D. B. Boyd, Eds., VCH, Weinheim, Germany, 1998, pp. 75-136. Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints. 

Kutteh, R., Straatsma, T.P. Molecular dynamics with general holonomic constraints and application to internal coordinate constraints. In Reviews in Computational Chemistry (eds... 

Entropic factors are a major problem for relatively large molecules. For organic macromolecules, the simulation of the probability W(S=k-In (W)) by molecular dynamics calculations or Monte Carlo simulations, has been used to calculate the entropy from fluctuations of the internal coordinates189"921. For simple coordination compounds the corrections based on calculated entropy differences are often negligible in comparison with the accuracy of the calculated enthalpies116,63,881. Therefore, the relatively easily available statistical term (Sstat) is usually the only one that is included in the computation of conformational equilibria (see Chapters 7 and 8). 

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