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)).
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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