[gmx-users] Output from gmx h2order
Christian Blau
blau at kth.se
Mon Nov 4 16:57:11 CET 2019
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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