gmx saxs


gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-d [<.dat>]] [-sq [<.xvg>]] [-b <time>] [-e <time>]
         [-dt <time>] [-xvg <enum>] [-ng <int>] [-startq <real>]
         [-endq <real>] [-energy <real>]


gmx saxs calculates SAXS structure factors for given index groups based on Cromer’s method. Both topology and trajectory files are required.


Options to specify input files:

-f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
-d [<.dat>] (sfactor.dat) (Optional)
Generic data file

Options to specify output files:

-sq [<.xvg>] (sq.xvg)
xvgr/xmgr file

Other options:

-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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)