[gmx-users] solvent orientation/sorient

[Stella Nickerson]

I want to calculate solvent orientation around two types of spherical
particle. The solvent has a long alkyl chain. I use sorient with three
atoms in the carbon chain in my index group, one at each end and one in the
middle. The results are confusing me.

Theta_1 is described as "the angle with the vector from the first atom of
the solvent molecule to the midpoint between atoms 2 and 3". Therefore (it
seems to me), if the alkyl chain is mostly sticking out perpendicular from
the surface of the spherical particle, theta_1 should be close to 0 and
cos(theta_1) should be close to 1. If the alkyl chain is more wrapped
around the spherical particle, parallel to the surface, theta_1 should be
closer to 90 degrees and cos(theta_1) should be closer to 0. However, when
I examine the two types of spherical particles visually and compare them to
the results from sorient, it seems to be the opposite--the system where the
alkyl chain looks (visually) more perpendicular to the particle surface has
lower cos(theta_1). Am I misunderstanding which angle exactly theta_1 is or
should I just trust the sorient calculation over what appears to me
visually?