Molecular Dynamics

Molecular dynamics consists of solving Newton's equations of motion

$$m_i{d^2x_i \over dt^2}(t) = -{\nabla}_{x_i}E_{TOTAL}$$ (11.1)

where the index $i$ runs through all free (i.e., not fixed) atoms and the gradient ${\nabla}_{x_i}E_{TOTAL}$ 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.