[gmx-users] Question concerning G_SAXS order parameter in mixed bilayers

Michal Skoczek ncskocze at cyf-kr.edu.pl
Tue Nov 4 15:39:32 CET 2014

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
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


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