[gmx-users] structure factor

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Tue Jan 29 04:04:52 CET 2013

В письме от 28 января 2013 16:06:20 пользователь Juliette N. написал:
> Dear all,
> I am trying to calculate structure factor or scattering density of a
> polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq  -n
> index

g_rdf can calculate SAXS structurefactor
g_sans  can calculate SANS structurefactor
> I provide an index file with System, Polymer (atom numbers of all polymers)
> and Solvent (all solvent molecules) groups.
> -startq      real   0       Starting q (1/nm)
> -endq        real   60      Ending q (1/nm)
> -energy      real   12      Energy of the incoming X-ray (keV)
> Are the calculations based on the 12 (keV) energy of the incoming x-ray?

In that caes yes.
> 1- I am wondering whether I should use System to obtain scattering denisty
> of the system or subgroups of polymer and solvent?

It depend on what you want. But beware that if you will use System or solvent 
group then you get structurefactor of the box
> 2- What is the difference between S(q) and scattering density? I guess in
> the command above, -sq gives S(q). How do I get scattering density then?

What kind of scattering density do you need? Xray? Neutrons?

Usualy its SLD = \dfrac{\sum b_i}{v_m}, where b_i is scattering length for i-
th atom, and v_m is molecular volume
> 3- Is there any other quantity related to structure factor that gromacs can
> estimate?

Other quantity is P(r) (g_sans for neutrons) or RDF (from g_rdf)
> I appreciate your time and patience.
> Best,
> Thanks,
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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