Geometric restraints

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Note You can superimpose harmonic restraining forces to interatomic distances, angles, or dihedrals that you have set up as named selections. Yon can also restrain atoms to points in space. See Using Geometric Restraints" on page SI and "Restraints" on page 105. 

See Using Geometric Restraints on page 81 for examples ofusing restraints. 

Certain geometrical restraints may be imposed, experimental data, for example, may indicate that some atom pairs are within a certain distance of each other. 

In the following discussion we will consider an ensemble of molecules that represents a liquid system. Assuming there is no correlation between molecular interactions and geometrical restraints, the partition sum Z of an ensemble can be factorized into three contributions ... 

Heterogeneous porous networks can be simulated taking into account characteristics proper of real media such as variations in pore size and connectivity. Real substrata display also physical or geometrical restraints that should be taken into account for an adequate modeling. Sorption characteristics can be studied in these simulated 3D networks. Comparison with actual isotherms of real porous media in order to infer or predict textural parameters should be the next step of this research. 

Likewise, the exact orientation of one or more ligand groups can sometimes remain uncertain. The choice of sensible geometric restraints for the refinement of non-standard groups, in particular the ligands, is not always trivial and... 

Lukaszewicz et al14 has postulated an "adsorptive" mechanism to explain the excellent retention of bacteria by membranes with some pores larger than the microorganism. He contends that the adsorptive sequestrations of the membrane are more important than the geometric restraints of sieving. 

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