[gmx-users] structure factor

[Juliette N.]

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

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?

1- I am wondering whether I should use System to obtain scattering denisty
of the system or subgroups of polymer and solvent?

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?

3- Is there any other quantity related to structure factor that gromacs can
estimate?


I appreciate your time and patience.
Best,

Thanks,