<br clear="all">Dear all,<br><br>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 <br><br>I provide an index file with
System, Polymer (atoms numbers of all polymers) and Solvent (all
solvent molecules) groups.<br><br>-startq real 0 Starting q (1/nm) <br>-endq real 60 Ending q (1/nm)<br>-energy real 12 Energy of the incoming X-ray (keV) <br><br>Are the calculations based on the 12 (keV) energy of the incoming x-ray?<br>
<br>1- I am wondering whether I should use System to obtain scattering denisty of the system or subgroups of polymer and solvent?<br><br>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?<br>
<br>3- Is there any other quantity related to structure factor that gromacs can estimate?<br><br><br>I appreciate your time and patience. <br>Best,<br><br>Thanks,<br>J. N.<br><br>