gmx rms compares two structures by computing the root mean square deviation (RMSD), the size-independent ρ similarity parameter (rho) or the scaled ρ (rhosc), see Maiorov & Crippen, Proteins 22, 273 (1995). This is selected by -what.
Each structure from a trajectory (-f) is compared to a reference structure. The reference structure is taken from the structure file (-s).
With option -mir also a comparison with the mirror image of the reference structure is calculated. This is useful as a reference for 'significant' values, see Maiorov & Crippen, Proteins 22, 273 (1995).
Option -prev produces the comparison with a previous frame the specified number of frames ago.
Option -m produces a matrix in .xpm format of comparison values of each structure in the trajectory with respect to each other structure. This file can be visualized with for instance xv and can be converted to postscript with gmx xpm2ps.
Option -fit controls the least-squares fitting of the structures on top of each other: complete fit (rotation and translation), translation only, or no fitting at all.
Option -mw controls whether mass weighting is done or not. If you select the option (default) and supply a valid .tpr file masses will be taken from there, otherwise the masses will be deduced from the atommass.dat file in GMXLIB. This is fine for proteins, but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned to unknown atoms. You can check whether this happend by turning on the -debug flag and inspecting the log file.
With -f2, the 'other structures' are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other.
Option -bin does a binary dump of the comparison matrix.
Option -bm produces a matrix of average bond angle deviations analogously to the -m option. Only bonds between atoms in the comparison group are considered.
