Keywords: manual

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## Restraints

An 'R' line should look like:

    R Form Modality Feature Group Numb_atoms Numb_parameters Numb_Feat (Modal2 Feat2 NumAt2 ...) Atom_indices Parameters

These parameters encode the restraints information as given in Section 5.3.

Here, `Form` is the restraint form type (see Table B.1). `Modality` is an integer argument to `Form`, and specifies the number of single Gaussians in a poly-Gaussian pdf, periodicity of the cosine in the cosine potential, and the number of spline points for cubic splines. `Feature` is the feature that this restraint acts on (see Table B.2.) `Group` is the physical feature type, and should be an index from Table 6.1. `Numb_atoms` is the total number of atoms this restraint acts on, `Numb_parameters` is the number of defined parameters, and `Numb_Feat` is the number of features the restraint acts on. `Numb_Feat` is typically 1, except for the multiple binormal (where it should be 2) and ND spline (where it can be any number). In cases where `Numb_Feat` is greater than 1, the modality, feature type, and number of atoms of each subsequent feature should be listed in order after `Numb_Feat`. (Note that `Numb_atoms` is the number of atoms acted on by the entire restraint, while `NumAt2` refers just to the atoms acted on by the 2nd feature.) Finally, the integer atom indices and floating point parameters are listed.

For example,

    R    3   1   1   1   2   2   1  437   28       1.5000    0.1000

will create a Gaussian restraint on the distance between atoms 437 and 28, with mean of 1.5 and standard deviation of 0.1.

Table B.1: Numerical restraint forms
Numeric form | Form type
1 | `forms.lower_bound`
2 | `forms.upper_bound`
3 | `forms.gaussian`
4 | `forms.multi_gaussian`
5 | `forms.lennard_jones`
6 | `forms.coulomb`
7 | `forms.cosine`
8 | `forms.factor`
9 | `forms.multi_binormal`
10 | `forms.spline` or `forms.nd_spline`
50+ | user-defined restraint forms

Table B.2: Numerical feature types
Numeric feature | Feature type
1 | `features.distance`
2 | `features.angle`
3 | `features.dihedral`
6 | `features.minimal_distance`
7 | `features.solvent_access`
8 | `features.density`
9 | `features.x_coordinate`
10 | `features.y_coordinate`
11 | `features.z_coordinate`
12 | `features.dihedral_diff`
50+ | user-defined feature types

Next: Excluded pairs Up: Restraints file Previous: Restraints file Contents Index