General propertiesΒΆ
To analyze some or all energies and other properties, such as total
pressure, pressure tensor, density, box-volume and box-sizes,
use the program gmx energy. A choice can be made from a
list a set of energies, like potential, kinetic or total energy, or
individual contributions, like Lennard-Jones or dihedral energies.
The center-of-mass velocity, defined as
\[{\bf v}_{com} = {1 \over M} \sum_{i=1}^N m_i {\bf v}_i\]
with \(M = \sum_{i=1}^N m_i\) the total mass of the system, can be
monitored in time by the program gmx traj -com -ov. It is however
recommended to remove the center-of-mass velocity every step (see
chapter Algorithms)!