[gmx-users] Regarding Cos theta functions calculations in gromacs...

Dilip H N cy16f01.dilip at nitk.edu.in
Thu Apr 13 11:27:50 CEST 2017


how do i calculate the cos theta distribution for water belonging to CH2
region of glycine....??

1] how to use the gmx sorient command.??, since it will be calculating two
angles between the vector from one or more reference positions of first
atom to each molecule...
why is it calculating two angles
θ_1: the angle with the vector from the first atom of the solvent molecule
to the midpoint between atoms 2 and 3.
θ_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.
2] how to make the indexes for it..??

With Best Regards,

Ph.D Student

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