Questions tagged [radial-distribution-function]

Questions about radial distributions functions: g(r).

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4 votes
1 answer
78 views

How to study the stability of structure in water and analyze the radial distribution function (RDF)?

Context: If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view. I would like to do the following: Confirm if the ...
2 votes
0 answers
41 views

Why I am seeing opposing trend in the partial PDF (pair distribution function) when compared to Total PDF?

I am working with x$\ce{M_2O}$-(1-x)$\ce{SiO_2}$ binary glass having two different fractions of modifier (x=0.2 and 0.4). Glass with a 40% modifier has a higher density than glass with a 20% modifier. ...
13 votes
1 answer
711 views

How to calculate RDFs for MD trajectories without PBC, directly from coordinates? [closed]

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a program that could calculate the radial distribution function from ion to oxygen (or ion to ...
6 votes
1 answer
83 views

Are all molecules under the same peak in g(r) always found in the same solvation shell?

For a liquid, the peaks in $g(r)$ are typically associated with the solvation shells: nearest neighbors, next-nearest neighbors, and so on. However, the $g(r)$ is averaging over many configurations, ...
3 votes
2 answers
243 views

How to quantify the lattice distortion from XRD?

In real crystals, the atoms may not always sit at their ideal lattice sites. How to quantify this lattice distortion? Based on my understanding from X-ray diffraction books, the Radial Distribution ...
9 votes
1 answer
305 views

How do you calculate a radial distribution function on a lattice?

For the radial distribution function $$g(r)=\frac{N(r)}{4\pi r^{2}dr \rho}$$ how do you do the calculation of the volume of the spherical shell in the denominator, $4\pi r^{2} dr$, when the simulation ...
9 votes
1 answer
2k views

How to calculate a structure factor from a radial distribution function?

I have been trying to take an FFT of the radial distribution function to calculate a structure factor. My understanding is this is the same as the regular FFT from the time to frequency domain. The ...
7 votes
0 answers
146 views

How to analyse structure factors calculated from a mixture of isotropic amorphous substrates

I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
5 votes
0 answers
458 views

Why calculation of coordination numbers from Element-specific RDFs (ASE) doesn't make sense? [closed]

The link to the trajectory is here.I am using the module and similar code of the ASAP calculator from ASE. The problem is as follows, the running Coordination Number doesn't match the number of atoms ...
5 votes
0 answers
607 views

How to get the coordination number from RDF in python ovito? [closed]

Basically, I am trying to get the running coordination number (CN), but the result isn't correct? I am multiplying the Radial Distribution Function (RDF) with ...
7 votes
0 answers
366 views

What's the pair correlation function? What information does it contain? [closed]

This question is related to this VASP tutorial, in which the pair correlation function (or radial distribution function: RDF) is utilized to justify whether the solid silicon is melt by AIMD (ab-...
5 votes
2 answers
184 views

How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter?

The problem is my box is not orthorhombic (base angles different than 90 degrees). So, I am getting wrong results with the formula, ...
7 votes
0 answers
108 views

Deriving relations for a hard sphere phase diagram [closed]

In Torquato's book "Random Heterogeneous Materials", he has written: $$\frac{p}{\rho kT} = 1+2^{d-1}\eta g_2 (D^{+})\tag{1}$$ where $g_2(D^+)$ is the contact value from the right-side of the ...
7 votes
1 answer
431 views

Radial distribution function for trajectories or time frame?

In many scripts I came across, I saw for the calculation of the RDF, both the trajectory and the individual timeframe also have been used. Can anybody help me with understanding how they are different ...
12 votes
1 answer
774 views

Normalization condition in evaluating the radial distribution function for a hard-spheres system

I am trying to simulate a 3D hard-spheres in a box system in Python. The idea behind this is that I have to create a system in a 1x1x1 box with periodic boundary conditions and with $N = 500$ ...
5 votes
1 answer
239 views

Have I missed something? RDF (radial distribution) script cannot capture the correct .xyz

I am trying to learn how RDF is working. To learn how RDF is working in practice I am testing the script (below) by printing all of the variables using this .xyz file example: I passed cartesian ...
11 votes
1 answer
2k views

How should I generate a radial distribution function (RDF) for an MD trajectory with python?

I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
11 votes
1 answer
1k views

How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?

I am simulating a droplet of water with GROMACS. The droplet consists of about 200 TIP3P water molecules and is placed near the center of a large, mostly empty box (...
21 votes
3 answers
887 views

Generating special quasirandom structures (SQS) for surface calculations?

Given that most of the available codes for performing DFT calculations work with periodic boundary conditions, there are tools like mcsqs as a part of the Alloy ...
12 votes
1 answer
2k views

Compute RDF between COMs of two selections (or groups) using GROMACS

I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...