[gmx-users] structure factor
joojoojooon at gmail.com
Sun Jan 8 02:04:28 CET 2012
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
I provide an index file with System, Polymer (atoms 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
I appreciate your time and patience.
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