Internal Coordinate Space

The Internal Variable Module (IVM) (Schwieters and Clore, 2001) is an efficient and flexible facility for dynamics and optimization of atomic coordinates. The IVM allows one to perform dynamics and optimization in torsion angle coordinates and also allows for rigid-body optimization, or mixed cases in which there are some free atoms, some rigid regions and other regions in which torsion angle are allowed to vary (Schwieters and Clore, 2001). More exotic internal coordinates can also be defined in the IVM. For example, one can allow bond angles to vary in addition to torsion angles in a fashion which is appropriate for ring pucker (e.g. proline rings in proteins and sugar rings in nucleic acids and carbohydrates). The IVM allows a choice of molecular dynamics integration algorithm, including ${\rm 6^{th}}$ order predictor-corrector algorithm which can automatically adjust timestep size, in addition to the usual velocity Verlet method. Cartesian gradient minimization remains useful in initial structure determination in order to achieve correct covalent geometries; one can then use a reduced set of internal coordinates for better efficiency

Examples of use of the IVM can be found in Clore and Bewley (2002) and Clore and Schwieters (2003).