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

[David van der Spoel]

Den 2020-01-27 kl. 01:28, skrev Iman Ahmadabadi:
> Dear Philip,
> 
> Yes, you are right, thank you very much for your time and kindness.
gmx trjconv -pbc whole

> 
> 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
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se