GSDG

GSDG or Gauss-Siedel Distance Geometry is a hybrid Krylov solver for distance geometry. It is related to the earlier Herman's minimizer used in programs like FRODO and CHAIN, but is more robust and has a stronger theoretical background. GSDG understands bond, angle, nonbon, and noel potentials. It can work on any combination of these terms. It systematically, one atom at a time, attempts to solve the distance equations. The non-bonded exclusion target is set to 4.5 Angstroms. This is too large and results in a distorted structure when the nonbonded terms are used. However this distorted structure is usually self-avoiding and readily corrected with conjugate gradients to result in a structure with both good geometry and self-avoidance.

GSDG is most useful for building simple small molecules, and adding moderate sized chucks to a partial structure.

GSDG is called as "gsdg n_cycles low_atom high_atom;". Only the number of cycles is required in which case all active atoms are searched. If only one atom is specified then only it is searched. Otherwise the range of atoms specified is searched. Gsdg checks the atom order and will not fail if high_atom low_atom is used.