NAME
gmx-saxs-legacy - Compute small angle X-ray scattering spectra
SYNOPSIS
gmx saxs-legacy [-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-legacy 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)
-
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)
SEE ALSO
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2025, GROMACS development team