On 02.06.2010, at 09:37, [email protected] 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 http://www.ruppweb.org/xray/comp/scatfac.htm 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) /Flo > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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