I have a question about plotting RDF.
I have a system including polymer and a functionalized CNT, and the simulation box is not rectangular. I used this simulation box to examine co2 adsorption.
For investigating the effect of F-CNT on adsorption, I want to use RDF, consider F-CNT as a group and CO2 as another group, and plot the RDF.
First, I went to use VMD, but at VMD, I got this error: ERROR) measure gofr: only orthorhombic cells are supported (for now).
This error alludes to my box’s angles!
Now, I am wondering if LAMMPS can give me the RDF for two different groups of molecules.
I read the manual; if I understand correctly, it seems LAMMPS gives us RDF for one type atom to another, not two different groups!
I would be grateful if someone could guide me on how I can get the RDF for two groups of molecules for the non-rectangular simulation box.
the g(r) function is defined for individual atoms and in the most strict sense only useful for bulk systems of individual atoms.
When you operate on “groups” you will basically get a superposition of the g(r) functions for the constituent atoms.
If that is not what you want, you first need to define what kind of distribution function you want to compute. It is not clear to me, how that would be defined for a F-CNT.
Thank you for your answer.
I want to check the effect of COOH on CNT on co2 adsorption.
So, I thought it would be a good comparison if I compared the RDF between CO2-CNT and CO2-F-CNT.
I don’t know if this method is correct or not; I am confused!
I can achieve RDF atom by atom, but it is not what I want!
For that you will first have to explain how this is defined.
A RDF is a rather simple measure that computes how likely it is to find a pair of atoms at a given distance compared to an ideal gas. For an ideal gas it would be a flat line at 1.
From that description it should be evident that what you want to compute must be defined differently since the objects you are comparing are not individual points. You have far more degrees of freedom like the orientation of the CO2 and that and the shape (length, diameter etc.) of the CNT.
Unless you can explain what you want to compute instead, nobody can help you.