[gmx-users] g_sorient

[Berk Hess]

>Ok, lets get it straight:
>first a vector is computed from the reference, either an atom or the centre 
>of mass of a group of atoms, to the first atom of the solvent.
>
>            H
>R  ----- O
>            H
>
>That would be a vector RO in this case. The other vector used for computing 
>theta1 is (for water) the dipole vector. Using the P1(cos(theta1)) then 
>gives me orientational preference of the water > dipole with respect to the 
>solvent. Theta2 is computed as the angle between > RO and the normal to the 
>water plane, which is as you say symmetric.
>

Yes.

>The only thing then is that you probably mean
>
> >no reason to use P2(cos(theta2)).
>
>                   P1 here.

Yes, sorry about that.
So we agree?

g_sorient -ro prints <cos(theta1)> and <3cos^2(theta2)-1> as stated
on the manual page (not <3cos^2(theta1)-1>).
These two numbers should give all the information about the
orientation of the solvent with respect to the solute.

Berk.





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