I would like to do an angular radial distribution function analysis to quantify the orientation of the aromatic rings in a solvent. Something like the figure below. The Manual says it’s possible but there’s no help in the gmx rdf doc on how to apply this.
[1] Basma, Nadir S., et al. “Local structure and polar order in liquid N-methyl-2-pyrrolidone (NMP).” The Journal of Physical Chemistry B 122.38 (2018): 8963-8971.
Hi,
With gmx rdf it is possible to calculate an angle dependent rdf gAB(r,θ), where angle θ is defined with respect to a certain laboratory axis, but I think this is not what you want.
Maybe you can see if gmx sorient can provide some useful information (with some tuning).
Kind regards
Alessandra
Thanks for your reply. However, gmx sorient doc is not well written and there’s no other explanation in the web about it. For example it says: “It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule” does it mean only the first atom of the solvent is considered? what if the ring is in the second atom of the solvent?
and also, should I give it all solvents’ molecules or only one?
It mean that the first atom of each solvent molecule. If the solvent is the water, the first atom of each water is the oxygen (if the atoms in a water molecule are ordered as OW, HW1, HW2)
I think there is no automatic way in which you can select who is the first atom. One alternative may be to create a gro and trj file where you have only the rings, then use them as input for gmx sorient -f trj -s gro
