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

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

9          gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                   [-d [<.dat>]] [-sq [<.xvg>]] [-b <time>] [-e <time>]
11                   [-dt <time>] [-xvg <enum>] [-ng <int>] [-startq <real>]
12                   [-endq <real>] [-energy <real>]
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DESCRIPTION

15       gmx saxs calculates SAXS structure factors for given index groups based
16       on Cromer’s method.  Both topology and trajectory files are required.
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OPTIONS

19       Options to specify input files:
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21       -f [<.xtc/.trr/…>] (traj.xtc)
22              Trajectory: xtc trr cpt gro g96 pdb tng
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24       -s [<.tpr/.gro/…>] (topol.tpr)
25              Structure+mass(db): tpr gro g96 pdb brk ent
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27       -n [<.ndx>] (index.ndx) (Optional)
28              Index file
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30       -d [<.dat>] (sfactor.dat) (Optional)
31              Generic data file
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33       Options to specify output files:
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35       -sq [<.xvg>] (sq.xvg)
36              xvgr/xmgr file
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38       Other options:
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40       -b <time> (0)
41              Time of first frame to read from trajectory (default unit ps)
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43       -e <time> (0)
44              Time of last frame to read from trajectory (default unit ps)
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46       -dt <time> (0)
47              Only use frame when t MOD dt = first time (default unit ps)
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49       -xvg <enum> (xmgrace)
50              xvg plot formatting: xmgrace, xmgr, none
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52       -ng <int> (1)
53              Number of groups to compute SAXS
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55       -startq <real> (0)
56              Starting q (1/nm)
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58       -endq <real> (60)
59              Ending q (1/nm)
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61       -energy <real> (12)
62              Energy of the incoming X-ray (keV)
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SEE ALSO

65       gmx(1)
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67       More    information    about    GROMACS    is    available    at     <‐
68       http://www.gromacs.org/>.
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71       2020, GROMACS development team
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762019.6                           Feb 28, 2020                      GMX-SAXS(1)
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