Molecular dynamics consists of solving Newton's equations of
motion
(11.1)
where the index runs through all free (i.e.,
not fixed) atoms and the
gradient
is derived from the
X-PLOR energy function (Chapter 4).
Presently, X-PLOR provides the option to
solve Eq. 11.1 in Cartesian coordinate space
(Section 11.1) or rigid-body coordinate space
(Section 11.2). Molecular dynamics
simulations can be stored as trajectory files.
Input format, output format, manipulations, and
analysis of trajectory
files are described in Section 11.