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, -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
