Rigid-body approximation

Since the rigid-body approximation gives only an upper bound for the translational friction coefficient and viscosity, MC values of the viscosity for ideal star... 

In many types of observations, for example, in the determination of X-ray structures, the molecule is approximated as a rigid body and is represented by an iconic (static) model. Of course, even supposedly rigid molecules are far from that Their atoms vibrate about time-averaged positions. Nevertheless, the choice of a static model under the rigid-body approximation is reasonable because the corresponding molecule occupies only a single minimum on the potential-energy hypersurface. 

Although in protein-protein docking the rigid-body approximation is still applied (Kimtz et al., 1982), in protein-ligand docking the small molecule is treated flexible. 

The bond increments, van der Waals radii, and well depths in equations (2-4) were determined from simultaneous least-squares fits to crystal structures, heats of sublimation, and in some cases gas phase dipole moments. In order to facilitate the derivation of these parameters and reduce the time required for fitting the crystal data, the molecules were treated a.s rigid bodies that are allowed to undergo translational and rotational motions within the crystal s unit cell. Due to the rigid body approximation the CFF nonbonded parameters can be parametrized and tested without a knowledge of the CFF intramolecular potential. 

This program is for a thermal motion analysis of the anisotropic displacement parameters (ADPs), is carried out in terms of the LST rigid-body approximation, and considers the correlations in the internal and overall motions. THMA is rewritten from the 1992 version of THMA14. ... 

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