10 votes
Accepted

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

As you suggesting, your computed $g(r)$ goes to zero at large $r$ because of your handling of the periodic boundary conditions. You should include every particle at a distance of $r$ whether it's in ...
Hebo's user avatar
  • 1,665
10 votes

Generating special quasirandom structures (SQS) for surface calculations?

First of all, it's better to define the terms here because probably not all the people here are familiar with SQS right away. SQS is an abbreviation for special quasirandom structures. The ...
Mithridates the Great's user avatar
9 votes
Accepted

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

You could fool the MDAnalysis RDF function InterRDF by setting an artificial cell of a size large enough so that the periodic boundary conditions don't cause any ...
Hebo's user avatar
  • 1,665
9 votes
Accepted

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

Here's an approach calculating it by hand with numpy. The coordinates are loaded from the trajectory using mdtraj in python: <...
lewiso1's user avatar
  • 936
8 votes
Accepted

Radial distribution function for trajectories or time frame?

If I understand your question correctly, you are saying that you have seen cases where time is included in the calculation of the radial distribution function (RDF). The RDF itself does not depend on ...
jheindel's user avatar
  • 3,534
7 votes

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

Without data to test exactly what you are doing it's difficult to say for absolute certain, but it looks to me that your main problem is that your first equation, the equation you are using for your ...
Ian Bush's user avatar
  • 775
6 votes
Accepted

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

As others have commented, discretization does not matter. Below you can see a picture that tries to explain this point. The $\mathrm{d}r$, or more correctly for the approximation we are making the $\...
Erik Kjellgren's user avatar
6 votes

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

Here are my two cents (things that I would try): How can I confirm the stability of the micelle? You could run the simulation for a longer time and/or run at different temperatures. Also, monitoring ...
Camps's user avatar
  • 22.9k
5 votes

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

The correct syntax is then the following: ...
gluuke's user avatar
  • 493
5 votes

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

Yes, it is possible for configurations which contribute to a particular peak in $g(r)$ to be outside of that solvation shell. As pointed out in the comments, this is only possible if you have a ...
jheindel's user avatar
  • 3,534
4 votes
Accepted

Can radial distribution function determine where the interactions of reference (atom/molecule) reduces greatly with surrounding atoms/molecules?

Your assumption regarding the RDF plot is generally correct. The RDF provides information about the probability of finding particles at a given distance from the reference atom/molecule. Analyzing the ...
Jaafar Mehrez's user avatar
4 votes
Accepted

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

Sticking with ase you can use the built-in get_distance function. It supports non-orthogonal unit cells. An example to get the distance between atom number ...
Hebo's user avatar
  • 1,665
3 votes

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

Ok, I think I figured out why your code is giving a straight line. This is too big to write as a comment, so I am putting this as answer. At the start of the function, you are determining the edges of ...
S R Maiti's user avatar
  • 6,741
3 votes

Generating special quasirandom structures (SQS) for surface calculations?

There are two different perspectives here. The first one is the creation of the SQS structure itself accomplished through the ATAT package, for example. The second one is the calculation of the slab ...
Anibal Bezerra's user avatar
3 votes

How to quantify the lattice distortion from XRD?

First of all it must be clarified that a lattice is a collection of geometrical point all characterized by a same surrounding (that is, each lattice point has the same number of nearest neighbour ...
gryphys's user avatar
  • 651
3 votes

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

Have you tried using the Ovito where there are built in functions to evaluate both RDF and CN of a system? Additionally, it might be possible to use Vesta to convert the unit cell to a rectangular one ...
PBH's user avatar
  • 2,653
1 vote

How to quantify the lattice distortion from XRD?

In my group we develop continuous symmetry and chirality measures that can be used to quantify the distortion of a structure, given the 3D coordinates. Please see: https://csm.ouproj.org.il/ See also ...
Inbal's user avatar
  • 11
1 vote

Generating special quasirandom structures (SQS) for surface calculations?

As Anibal points in his answer, generating the SQS and using it for a surface calculation are two separate things, and shouldn't affect each other. You would still take all precautions as usual while ...
Hitanshu Sachania's user avatar

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