gmx saxs
Synopsis
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>]
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 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)
- 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>
- 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)