[gmx-users] gmx_dipoles Mtot and aver difference

Justin Lemkul jalemkul at vt.edu
Sat Aug 25 13:54:40 CEST 2018

On 8/25/18 7:51 AM, Raag Saluja wrote:
> Hi!
> I had written earlier that I wanted to compare the dipole moments of a few
> proteins and that the Mtot and Aver files were giving me diametrically
> opposite results. The proteins with the highest dipole moments according to
> Mtot were the ones with the lowest dipole moments according to aver and
> vice-versa. I had asked what the difference was between the two files and
> why I was getting such results.
> David had very kindly replied that I should center the protein and had
> asked whether my proteins were neutral.
> I did use genion and -neutral command to neutralise the system. I  had also
> centered the protein. Still I get this result.

The overall charge of the *system* does not matter if you are computing 
the dipole properties of the *protein*. If the protein has a net charge, 
it must be re-center such that the center-of-charge is at the coordinate 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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