1GMX-SAXS(1) GROMACS GMX-SAXS(1)
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6 gmx-saxs - Compute small angle X-ray scattering spectra
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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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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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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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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 2022, GROMACS development team
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762022.2 Jun 16, 2022 GMX-SAXS(1)