General properties

gmx energy, gmx traj

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

(1) $${\bf v}_{com} = {1 \over M} \sum_{i=1}^N m_i {\bf v}_i$$

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)!