[gmx-users] Output from gmx h2order

[Christian Blau]

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