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318 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 ...
547 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 ...
158 views

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

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 ...
531 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. ...
364 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 (...
123 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 $N = 500$ ...
76 views

Normalizing the radial distribution function [closed]

The radial distribution function is defined as: $$g(r)=\frac{dn}{4\pi r^{2} dr \rho}.\tag{1}$$ Why, in the calculation, do you divide twice by the number of molecules? What I mean is something like ...
74 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-...
78 views

Deriving relations for a hard sphere phase diagram

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 ...
68 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 ...
50 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 ...
69 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, ...
62 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 ...