g_saxs1
Compute small angle x-ray scattering spectra
Part of gmx-saxs(1).
Usage
gmx saxs
[-f
[<.xtc/.trr/ ...
>]]
[-s
[<.tpr/.tpb/ ...
>]]
[-n
[<.ndx>]]
[-d
[<.dat>]]
[-sq
[<.xvg>]]
[-nice
<int>]
[-b
<time>]
[-e
<time>]
[-dt
<time>]
[-xvg
<enum>]
[-ng
<int>]
[-startq
<real>]
[-endq
<real>]
[-energy
<real>]
Overview
gmx saxs calculates SAXS structure factors for given index groups based on Cromer's method. Both topology and trajectory files are required.
Options
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-d [<.dat>] (sfactor.dat) (Input, Optional)
Generic data file
-sq [<.xvg>] (sq.xvg) (Output)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-ng <int> (1)
Number of groups to compute SAXS
-startq <real> (0)
Starting q (1/nm)
-endq <real> (60)
Ending q (1/nm)
-energy <real> (12)
Energy of the incoming X-ray (keV)