Thank you for your reply. I should have chosen "Input coordinate of two points to define a line", or set the extension distance to 0 before using "Input index of two atoms to define a line". Thank you again for your help.

If you choose two atomic nuclei to define the line to be plot in Multiwfn, then the value of X-axis will corresponds to the distance from starting point, which is irrelevant to Cartesian coordinate of the atoms.

I am trying to plot the electron density of a water dimer along the O-O bond. The geometry of this is as follows in Q-Chem input format with unit in Angstrom:

$molecule
0 1
--
0 1
O      0.000000    0.000000    0.000000
H      0.480763   -0.756792   -0.334637
H      0.480763    0.756792   -0.334637
--
0 1
O      0.000000    0.000000    2.900000
H     -0.899690    0.000000    3.225430
H     -0.089397    0.000000    1.947180
$end

I was able to generate the line density along the O-O bond with Multiwfn, however, it seems like the molecule was shifted so the nuclei aren't in the initial position as input. I was able to confirm this conjecture by comparing the z coordinate and the X position in the curve graph in the saved line.txt file. Is there a way to fix the position of the molecule when generating the line density plot? Thank you in advance for your time!