Rigid-Body Coordinate Space

After completion of the molecular dynamics calculation, the partial energy terms for the last molecular dynamics step are stored in the appropriate symbols. The name of the symbols is given by $energy-term (see Section 4.5). The overall energy (Eq. 4.1) is stored in the symbol $ENER; the rms gradient is stored in $GRAD. The value of the second energy function (Eq. 4.26) is returned in the symbol $PERT. In addition, the following symbols are declared: $TEMP, $TOTE, and $TOTK, which are respectively the temperature, total energy, and kinetic energy.

X-PLOR's implementation of rigid-body molecular dynamics
follows the algorithm described by Head-Gordon and Brooks (1991).
The algorithm treats each group as a continuous mass distribution
located at the center-of-mass position defined by

(11.11) |

(11.12) | |||

(11.13) |

Here the index J labels the rigid bodies, and the summation index runs over all atoms comprising a particular group.

- Initialization
- Iteration
- Syntax of the Dynamics Rigid Statement
- Requirements
- Example: Run a Rigid-Body Dynamics Simulation