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) |
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 three-step Verlet method
(Verlet, 1967).
Xplor-NIH 2024-09-13