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##

Finite Difference Approximation

X-PLOR makes use of a third-order
finite difference approximation in
(Brünger, Brooks, and Karplus, 1984).
First, the initial coordinates are subjected to the SHAKE method.
Then the system gets the initial velocities . Next,
the program prints the energy of the initial coordinates. A two-step
method is used to obtain the coordinates :
(11.8) |

Iteration from step to step causes
.
The algorithm computes the forces
.
The algorithm then computes

(11.9) |

(11.10) |

*Xplor-NIH 2024-09-13*