Dear Gromacs Users, I am trying to calculate x ray structure factor for my system using this GMX SAXS (g_saxs) utility. I am using GROMACS ver. 5.0.2.
What I am expecting is to obtain results similar to this (http://www.cell.com/cms/attachment/578237/4320295/gr2.gif) This figure is from this publication ( http://www.sciencedirect.com/science/article/pii/S000634950573157X ). Unfortunately I am obtaining something totally different - a single peak described as the "Scattering intensity" ("Q 1/nm" on the X asis and "Intensity a.u." on the Y axis). I have a few questions: 1)Am I doing something wrong? The curve looks totally different than the one in the paper. Should it be recalculated somehow? 2) Why there are just a few points calculated ? I have tried to add options -grid and -bin to obtain more points but it changes nothing. My command looks like this: g_saxs -f sys_13.xtc -s sys_13.tpr -n index.ndx -startq 0 -endq 5 -energy 12 -b 49000 -e 50000 3) Selecting the single molecule type in index file or the whole system without water does not change the way the curve looks like. Should I select whole system with water? Please give me some advice on that; I would be very grateful. Thank you all! Best regards Michal -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
