[gmx-users] Correct use of gmx traj -mol ?

[James]

Hi,

I am interested in obtaining temperature readings that are corrected for
velocity (meaning, if a molecule has a net velocity, that kinetic energy
should not be counted as part of temperature). I suspect this is what the
traj -mol option would do, but I can't get it to run without error.

I am guessing the problem lies with my index files. The traj docs state
that "When -mol is set, the numbers in the index file are interpreted as
molecule numbers...". I don't understand this. All my index files contain
are group headings and atom numbers. It seems like there would need to be
another column that indicates molecule number (and I know such a column
exists in some other file formats, but nothing I've read indicates that
.ndx files can have extra columns).

Any idea what I am doing wrong, or can anyone provide a set of test file on
which "gmx traj -mol" can be successfully run?

Sincerely,
James