Geometrical restraints

With the help of the distance restraints DFIX and DANG, the distance between two atoms can be restrained to possess any target value. The syntax for bond distance restraints is 

The similarity restraint SADI restrains the distance between two (or more) pairs of atoms to be equal within a default standard uncertainty s of 0.02 A, no matter what that distance might be. The syntax is similar to DFIX / DANG, except that no target value for the distances is specified  

If you have a reason to assume that the distance between the atoms C(l) and C(2) should be similar to the distance between the atoms C(7) and C(8), the appropriate command line would read  

the default standard uncertainty of 0.02 A can be changed by introducing its new value as s between SAD I and the first atom. Notice that this restraint requires atom pairs, hence the number of atom names needs to be even. 

With the help of SAME, the geometry of two or more groups of atoms can be restrained to be similar. This can be convenient when a structure contains several crystal-lographically independent but geometrically equivalent molecules or ligands. The SAME command generates the necessary SADI restraints with appropriate standard uncertainties (0.02 A for 1,2-distances and 0.04 A for 1,3-distances) for equivalent molecules or parts of molecules. It is a very powerful restraint but particularly error-prone, since it requires both the atoms named with the restraint and the atoms following the SAME command in the. ins file to be in the correct order. The syntax as well as the benefits and pitfalls of SAME are explained in Chapter 5. 

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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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