Partially rigid models

Partially rigid models In the general case of a molecular model that is only partially rigid (i.e., has more than six degrees of freedom, if nonlinear) ... 

Many properties of polymer solutions are well explained in terms of the freely-jointed-chain model. The present work constitutes a part of a program of study of polymer chains in solution which are partially rigid (or partially flexible). 

Each of these two approaches is in principle applicable to molecular models of both the types encountered in MD simulations the totally rigid molecular models used in simulations of, for example, nitrogen and water, and the partially rigid molecular models (i.e., where only some of the internal degrees of freedom are constrained) used in early simulations of butane, for example. In practice, the first approach above is truly effective only when applied to totally rigid molecular models, whereas the second approach is equally effective for molecular models of both types, as described next. 

The experimental and hypothetical crystal structures are superimposed in Figure 6.9 using the COMPACK algorithm. The RMS deviation between these structures is fairly small. The W99 potential with the multipole description of the electrostatics, after a minimization of the structures using a partial rigid body model and the DREIDING potential, is a potential good model for this systan. 

In the rigid model of Shim et al., the united atom representation for the CH2 and CH3 groups is used. Hence, the cation is represented by a rigid body and its geometry (bond lengths, angles) was taken from experimental x-ray diffraction data obtained from crystals of [C2-mim][Br] (Elaiwi et al., 1995). The electrostatic description of the cation consists of fixed partial charges centred on the atoms (Hanke et al., 2001). The interaction potential in the system is represented by a sum of pairwise additive interatomic LJ and Coulombic potentials ... 

Figure 4 Time step dependence of the average total energy for two models of a partially hydrated dodecamer DNA duplex. Thinner traces show results for virtually harmonic conditions when temperature was lowered to 1 K. The DNA molecule has fixed bond lengths, rigid bases, and fixed valence angles except for the mtra- and extracyclic bond angles m sugars, (a) No modifications of inertia (b) inertia modified as explained m the text. (From Ref. 54.)...

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