> 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
Thx for ans! I have already done this. I also modify sfactor.c a little to select atoms acording to atom number instead of atom name ;-) But `g_rdf -sd` gives me plot of 'absorbtion units' versus 'reverse nanometers'. And it looks absolutely different from structure factor from article I cited. For example in article SF is fading sinusoid while g_rdf gives me positive increasing curve. I suppose it's diffraction spectrum, not structure factor. Or ... ? (i rly have no idea, so i'm scanning source code of sfactor.c now, but may be anybody know what `g_rdf -sd` exactly do?? ) Thanx before, comcon1) -- 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
