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283 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 ...
478 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 ...
426 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. ...
292 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 (...
113 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 $N = 500$ ...
72 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 ...
65 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 ...
65 views

### Normalizing the radial distribution function

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 ...
105 views

### How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

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