[gmx-users] gmx sorient interpretation
mark.j.abraham at gmail.com
Tue May 2 11:34:58 CEST 2017
On Mon, May 1, 2017 at 9:40 PM Marcelo Depólo <marcelodepolo at gmail.com>
> I am not sure how to interpret the cos(theta1) around my reference atom.
> The help printed is not straightforward when comes to set which atoms forms
> the angle theta1. For instance.
> "theta_1: the angle with the vector from the first atom of the solvent
> to the midpoint between atoms 2 and 3.
> theta_2: the angle with the normal of the solvent plane, defined by the
> three atoms, or, when the option -v23 is set, the angle with the vector
> between atoms 2 and 3."
> In case of water (using default Water group), is oxygen the atom 1 and the
> hydrogens the atoms 2 and 3? Does it follows the index given by .tpr used
> for analyses?
I don't know. I suggest you make an index group of one water molecule, run
gmx sorient, then change the order of the indices and see if that changes
the result. If it does, then it's the order of the index group (which I
expect is the case). Otherwise, it's the order of the input configuration
(which defines default index groups). Let us know and I'll update the docs.
If so, the distribution as a function of distance gives positive and
> negative values for cos(theta1). Does positive values means that water
> oxygen is orient towards my reference at that distance?
"Towards" is too vague to be a useful definition. Hence the geometric
specifics. And of course -cos(theta) does not equal cos(-theta).
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