[gmx-users] g_sorient

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 23 00:05:10 CEST 2002

On Mon, 22 Apr 2002, Berk Hess wrote:

>Your question is not completely clear, as you use theta for the angle,
>whereas g_sorient calculates two angles, theta1 and theta2.
>P2 is only used for cos(theta2), where theta2 is the angle with the
>normal of the solvent plane. For symmetric solvent molecules (such
>as water) the sign of cos(theta2) is meaningless, therefore
>P1(cos(theta2)) is meaningless. Even for asymmetric molecules I see

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.

R  ----- O

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.

The only thing then is that you probably mean 

>no reason to use P2(cos(theta2)).

                  P1 here.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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