$r$	Bond length
$\theta$	Bond angle
$\varphi$	Proper dihedral angle
$r_0$	Reference bond length
${\theta }_0$	Reference bond angle
${\varphi }_0$	Reference proper dihedral angle
$K_r$	Force field parameters related to bond length
$K_{\theta }$	Force field parameters related to bond angle
$V_n$	Force field parameters related to proper dihedral angle
q	The charge of the atom
$r_{ij}$	The intermolecular distance of atoms i and j
$\sigma$	The length parameters
$\epsilon$	The energy parameters
$m_{ia}$	The mass of atom $a$ of molecule i
${\mathbf{r}}_{ia}$	The position of atom $a$ of molecule i
${\mathbf{p}}_{i\alpha }$	The momentum of atom $a$ of molecule i
$M_i$	The mass of the center of mass of molecule i
$r_i$	The position of the center of mass of molecule i
$p_i$	The momentum of the center of mass of molecule i
$y_i$	The y components of molecule i
$p_{yi}$	The momentum of y components of molecule i
${\mathbf{F}}_{ia}$	The sum of all forces on atom $a$ of molecule i due to interaction potentials
${\mathbf{F}}_{\mathit{ia}}^{\mathrm{C}}$	All forces on atom α of molecule i due to any constraint forces that may be present
i	The x-unit vector
ζ	The thermostat multiplier
$\langle P_{xy}\rangle$	The xy component of the pressure tensor P
$\dot{\gamma }$	The strain rate