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gmx-saxs(1)                     GROMACS Manual                     gmx-saxs(1)

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

SYNOPSIS
       gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                [-d [<.dat>]] [-sq [<.xvg>]] [-nice <int>] [-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 and output files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Input)
           Trajectory: xtc trr cpt trj gro g96 pdb tng

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Input, Optional)
           Index file

       -d [<.dat>] (sfactor.dat) (Input, Optional)
           Generic data file

       -sq [<.xvg>] (sq.xvg) (Output)
           xvgr/xmgr file

       Other options:

       -nice <int> (19)
           Set the nicelevel

       -b <time> (0)
           First frame (ps) to read from trajectory

       -e <time> (0)
           Last frame (ps) to read from trajectory

       -dt <time> (0)
           Only use frame when t MOD dt = first time (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
       gromacs(7)

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

VERSION 5.0.6                                                      gmx-saxs(1)