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| GMX-SAXS(1) | GROMACS | GMX-SAXS(1) |
NAME
gmx-saxs - Compute small angle X-ray scattering spectraSYNOPSIS
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)
- 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
gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2022, GROMACS development team| January 14, 2022 | 2021.5 |
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