Analysis

System check

It is also a good idea to look at the energies and pressure of your simulation, best already during the simulation! If something goes wrong you can realize it before you spent all the precious computing time. Gromacs enables you to check your system with its energy and traj tools.

gmx energy: Extracts energy components or distance restraint data from the energy file. The user is prompted to interactively select the energy terms or other quantities. See all accepted options with gmx energy -h.

gmx energy -f md.edr -o system_term.xvg

You can select the term you want from the returned list. You can look at the energies and other properties, such as total pressure, pressure tensor, density, box volume, and box sizes. Moreover, energies can be split into contributions, like potential, kinetic or total energy, or individual contributions, like Lennard-Jones or dihedral energies.

gmx trjconv: Can convert trajectory files in many ways. Here, a number of options are chosen to change the periodicity representation such that the protein is relocated as a whole into the unit cell:

gmx trjconv -f md.trr -s md.tpr -o md_protein.trr -center -ur compact -pbc mol

gmx traj: Plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each group.

gmx traj -f md_protein.trr -s md_protein.tpr -com -ox coordinates.xvg -ov velocities.xvg -of forces.xvg