Hi Magnus,

thanks for looking at it, I just wrote a ticket.

Just for everybody who’s interested:

**I tested this (below) and there indeed seems to be problem in gmx dipoles, that for charged molecules/systems a wrong dipole is determined.**

I used a trajectory a two-atomic CO molecule (GROMACS 2021.5; same result for earlier versions; the newest version still seems to use COM - gromacs/src/gromacs/gmxana/gmx_dipoles.cpp at 3ffa4ddb141f847edbcd42c9fa88dc820ad70b0b · gromacs/gromacs · GitHub). Keeping the coordinates of the initial trajectory, I added or subtracted the net charge. In that way, having the same geometry, I had two cases with similar charge separation:

Case 1 - net charge = 0:

q_C = 0.633601

q_O = -0.633601

Case 2 - net charge = -1:

q_C = 0.133601

q_O = -1.133601

Assuming correct treatment of dipoles, GROMACS should give the same result since net charge is subtracted. However, results are different:

For case 1, GMX DIPOLES gives me:

## Dipole moment (Debye)

Average = 3.6924 Std. Dev. = 0.0656 Error = 0.0001

The following averages for the complete trajectory have been calculated:

Total < M_x > = 0.365268 Debye

Total < M_y > = 0.08411 Debye

Total < M_z > = -0.0795452 Debye

Total < M_x^2 > = 4.49683 Debye^2

Total < M_y^2 > = 4.21801 Debye^2

Total < M_z^2 > = 4.92327 Debye^2

Total < |M|^2 > = 13.6381 Debye^2

Total |< M >|^2 = 0.146823 Debye^2

< |M|^2 > - |< M >|^2 = 13.4913 Debye^2

Finite system Kirkwood g factor G_k = 0.989547

Infinite system Kirkwood g factor g_k = 0.9745

Epsilon = 1.0478

In Case 2, I obtain:

## Dipole moment (Debye)

Average = 7.4619 Std. Dev. = 0.1802 Error = 0.0002

The following averages for the complete trajectory have been calculated:

Total < M_x > = 0.775687 Debye

Total < M_y > = 0.105891 Debye

Total < M_z > = -0.0110759 Debye

Total < M_x^2 > = 18.5724 Debye^2

Total < M_y^2 > = 17.3047 Debye^2

Total < M_z^2 > = 19.8354 Debye^2

Total < |M|^2 > = 55.7125 Debye^2

Total |< M >|^2 = 0.613027 Debye^2

< |M|^2 > - |< M >|^2 = 55.0995 Debye^2

Finite system Kirkwood g factor G_k = 0.989573

Infinite system Kirkwood g factor g_k = 0.935698

Epsilon = 1.19521

Best,

Jacek