[gmx-developers] Query about the detailed algorithm used when calculating the structure factor using 'g_rdf -sq'

Mark Abraham mark.j.abraham at gmail.com
Mon Nov 17 19:08:53 CET 2014


On Mon, Nov 17, 2014 at 6:05 PM, Junju Mu <mjju1206 at gmail.com> wrote:

> Dear Developers,
> Gentle greetings. I would firstly thank you for your hard work in building
> such a great package for simulations. Thank you!
> I have recently calculated the structure factor for my systems using
> 'g_rdf -sq' option, and wanted to compare my profiles to those from
> experiment papers. However, I could not find the detailed algorithm for
> this calculation. What I could find is it used FFT (fast Fourier transform)
> algorithm, but I could not find out what exactly the equations were.
> I wonder if you could kindly show me the detailed equations for doing the
> 'g_rdf -sq' option, so that I could know what should I do with my results.

It's an unpleasant truth, but the best/only documentation is probably the
source code. But at least you can see it! In src/gromacs/gmxana/gmx_rdf.c
you can find pretty much all there is to see. Do ask if you find something
there that's too impenetrably cryptic!


Thank you in advance!
> Best wishes,
> Junju
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