gmx-saxs (1)

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>]

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 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)

gromacs(7)

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