[gmx-users] Output from gmx h2order

[Decai Yu]

Christian
Thank you very much.
That is very helpful.
Decai

On Mon, Nov 4, 2019 at 10:57 AM Christian Blau <blau at kth.se> wrote:

> Hello Decai,
>
>
> h2order works in the following way:
>
>    - all water molecules are put into the simulation box by applying
> periodic boundary conditions so that the first
> water molecule atom is in the simulation box
>
>    - the simulation system is sliced along z (0,0,1) direction (default,
> can be changed)
>
>    - each water molecule contributes it's dipole to the slice sum of
> dipole moments - this is what you see in the output
> columns mux, muy, muz. These dipoles are calculated as  \sum charge *
> positionVector. The dipole moments are averaged
> per slice over all water molecules and frames
>
>    - the cosine with normal is calculated as the average normalized inner
> product of the dipole vector with the "normal"
> - in the default case z direction, .e.g, average[dipole . (0,0,1) /
> sqrt(dipole.dipole)]
>
>
> Best,
>
> Christian
>
>
>
> On 11/1/19 8:00 PM, Decai Yu wrote:
> > Hi, All
> > There are four columns from the output of gmx h2order, mux, muy, myz,
> > cosine with normal.
> > What are they? Can anyone further explain?
> > Decai Yu
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