[gmx-users] gmx sorient interpretation

Marcelo Depólo marcelodepolo at gmail.com
Mon May 1 21:40:32 CEST 2017


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 same
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?

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?


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