 | Xplor-NIH home Documentation |
Next: Syntax of the Dynamics Up: Molecular Dynamics Previous: Example: Run a Rigid-Body
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 
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).
Subsections
Next: Syntax of the Dynamics Up: Molecular Dynamics Previous: Example: Run a Rigid-Body Contents Index