Synopsis
gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-d [<.dat>]] [-sq [<.xvg>]] [-nice ] [-b
Description
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)
