Molecular dynamics consists of solving Newton's equations of motion
where the index i 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. 10.1 in Cartesian coordinate space (Section 10.1) or rigid-body coordinate space (Section 10.2). Molecular dynamics simulations can be stored as trajectory files. Input format, output format, manipulations, and analysis of trajectory files are described in Section 10.