masses file contains all the correspondences between atomic labels or names, as given in the trajectory file, and the mass of those atoms. The units are atomic mass units (amu). The atomic label should be followed by the mass value, and one atom definition is given on each line.
For instance, if one has a water sample and the labels for H and O as given in the trajectory file are
OW, respectively, the corresponding
masses file would look like this:
HW 1.01 OW 16.00
If different labels are given for identical atoms, then all of the labels must have an explicit definition attached. For example, if instead of one single H label for both Hs in a water molecule, two different labels are used,
HW2, this must be made explicit in the
HW1 1.01 HW2 1.01 OW 16.00