[gmx-developers] Total dipole incorrect in energy file

[Berk Hess]

Hi,

We can't make molecules whole in the general case with DD.
But also the dipole moment will only make sense for systems without
molecules with net charge.
So I think we should remove it from the energy file.
This will mean that we can not append to old energy files, you will get
a fatal error in that case.

Berk

David van der Spoel wrote:
> Hi,
>
> it used to be so that mdrun did not break molecules. However, nowadays
> it does, even though they are fixed before writing the coordinates. I
> suspect however that the broken molecules are not fixed before
> computing the total dipole, which is stored in the energy file. The
> total dipole is used for computing the dielectric constant in g_dipoles.
>
> With the current g_dipoles I get good dielectric constants when using
> the coordinates, and insane (500) when using the energy file.
>
> If this observation is correct we can do two things:
> - fix the coordinates at every step before computing the total dipole
> - not compute abd save the total dipole at all and remove the -en
> option from g_dipoles
>
> I guess the decision depends on whether the CPU time for reconstrucing
> the molecules before computing the total dipole is large or not. Maybe
> Berk can comment on that, obviously there is a reason for not doing it
> every step.
>