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Cartesian restraints interface

This interface serves as a modifier for other calculations. It allows to restrain atoms or groups (represented by their center of mass) in cartesian coordinates. Multiple restrains can be used in a calculation. Each restraint acts on a group of atoms (specified by a selection expression) as a harmonic potential. The potential can have a flat bottom of radius given by r_plateau, above the radius, force constant defines the energy and gradient. The center (equilibrium position) of the restraint can be set to specified coordinate, origin of coordinate system or initial position of the group.

In the input, keyword cartesian_restraints is used to define the restraints. It expects YAML representation of an array of restraint definitions. The input can look like:

  - selection: "1"
    center: coord(5,5,-5)
    r_plateau: 2.0
    fconst: 20
  - selection: ":2"
    center: origin
    r_plateau: 0.0
    fconst: 200
  - selection: ":3-10"
    center: initial
    r_plateau: 0.0
    fconst: 200

Here, atom 1 is restrained to a region 2 angstrom around point [5,5,-5] (using a flat-bottom potential). Residue 2 is restrained to the origin of coordinates and a group of residues 3 to 10 is restrained to its original position (defined by center of mass of the group).