X-PLOR makes use of a third-order
finite difference approximation in **dt**
(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 :

IF SHAKE constraints are present, the SHAKE method is applied to with respect to .

Iteration from step **n** to step **n+1** causes
.
The algorithm computes the forces .
The algorithm then computes

If required, the SHAKE method is applied to with as the reference set. Finally, the velocities at this step are computed:

(The velocities do not enter the equations to compute the trajectory .) In case of zero friction coefficients , this algorithm reduces to the three-step Verlet method (Verlet 1967).

Sat Mar 11 09:37:37 PST 1995