[gmx-users] Discrete structure factor from g_rdf

Florian Dommert dommert at icp.uni-stuttgart.de
Wed Jun 2 17:19:07 CEST 2010

On 02.06.2010, at 09:37, comcon1 at erg.biophys.msu.ru wrote:

> I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
> according to the article:
> http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
> I have several corrected OPLS all-atom bilayer models and I need to
> validate my model according to experimental x-ray diffraction data. But I
> can't understand, how '-sq' property of g_rdf can helps me to compute
> structure factor.. May be anybody have some experience in this theme?

 So far I also haven't really used g_rdf to calculate the structure factor of a system, so I can't give you a hint how to reproduce the results in the paper. However as the version of g_rdf in the current and earlier release was not able to treat every atomtype perhaps you should at first consider the git version of g_rdf for your calculations. This version is capable of treating every atomtype if you supply the corresponding data. The calculation is based on a so called Cromer-Mann fit that requires different parameters for different atoms. This parameters can be for example obtained from 


There is a reference to an article and a short introduction contained on the website.

Finally append your parameters to the list in share/top/sfactor.dat and use the corresponding flag in the command line ( g_rdf -h will tell you which)

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Florian Dommert

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
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EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

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