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GMX-SAXS(1) GROMACS GMX-SAXS(1)

gmx-saxs - Compute small angle X-ray scattering spectra

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:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file
Generic data file

Options to specify output files:

xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Number of groups to compute SAXS
Starting q (1/nm)
Ending q (1/nm)
Energy of the incoming X-ray (keV)

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

2019, GROMACS development team

February 15, 2019 2019.1