[gmx-users] Dipole moment and dielectric constant - gmx dipoles

Iman Ahmadabadi imanahmadabadi75 at gmail.com
Mon Jan 27 01:29:04 CET 2020


Dear Philip,

Yes, you are right, thank you very much for your time and kindness.

Best regards,
Iman

On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi <imanahmadabadi75 at gmail.com>
wrote:

> Dear Gromacs users,
>
> I'm trying to reproduce the gmx dipoles results via python code. In
> calculating the fluctuations of total dipole moment, which is the sum on
> dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
> which the charges q_{i} are in electron unit and position R_{i} are in nm.
> For calculating M for each time step (frame), the x,y, and z component of
> each atom is multiplied to their charges, and then summing on all atoms.
> The average of M is on all trajectory frames, meaning that summing on M for
> all frames and then dividing by the number of frames. Here, the acquired M
> is divided by proper constant (0.020819434 e
> <https://en.wikipedia.org/wiki/Elementary_charge>·nm
> <https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
>
> For M^{2}, M.M (dot product of M by M) is calculated for each frame and
> then summing on all frames, followed by dividing by the number of frames.
> But the results are larger than gmx dipoles, I wanted to ask that there is
> something gmx dipoles is using in order to calculate the <M> and <M^2>,
> causing this difference? I appreciate any help in this regard.
>
> Best regards,
> Iman
>


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