Finite Difference Approximation
XPLOR makes use of a thirdorder
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 twostep
method is used to obtain the coordinates :

(11.8) 
IF SHAKE constraints are present,
the SHAKE method is applied to with respect to .
Iteration from step to step causes
.
The algorithm computes the forces
.
The algorithm then computes

(11.9) 
If required, the SHAKE method
is applied to with as the
reference set. Finally, the velocities at this step are computed:

(11.10) 
(The velocities do not enter the equations to compute the
trajectory .) In case of
zero friction coefficients , this algorithm
reduces to the threestep Verlet method
(Verlet, 1967).
XplorNIH 20231110