GMX-SCATTERING(1)

NAME
gmx-scattering - Calculate small angle scattering profiles for SANS or SAXS

SYNOPSIS

    gmx scattering [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
                 [-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
                 [-dt <time>] [-tu <enum>] [-fgroup <selection>]
                 [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
                 [-selrpos <enum>] [-seltype <enum>] [-sel <selection>]
                 [-startq <real>] [-endq <real>] [-qspacing <real>]
                 [-binwidth <real>] [-mc-coverage <real>] [-seed <int>]
                 [-[no]norm] [-[no]mc] [-scattering-type <enum>]

DESCRIPTION

gmx scattering calculates SANS and SAXS scattering curves using Debye method.

The scattering intensity, I(q), as a function of scattering angle q with averaging over frames.

Note that this is a new implementation of the SANS/SAXS utilities added in GROMACS 2024. If you need the old ones, use gmx sans-legacy or gmx saxs-legacy.

OPTIONS

Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md

-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Input structure: tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)
    Extra index groups

    Options to specify output files:

-o [<.xvg>] (scattering.xvg) (Optional)
    scattering intensity as a function of q

    Other options:

-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 if t MOD dt == first time (ps)

-tu <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s

-fgroup <selection>
    Atoms stored in the trajectory file (if not set, assume first N atoms)

-xvg <enum> (xmgrace)
    Plot formatting: xmgrace, xmgr, none

-[no]rmpbc (yes)
    Make molecules whole for each frame

-[no]pbc (yes)
    Use periodic boundary conditions for distance calculation

-sf <file>
    Provide selections from files

-selrpos <enum> (atom)
    Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

-seltype <enum> (atom)
    Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

-sel <selection>
    Selection for Scattering calculation

-startq <real> (0)
    smallest q value (1/nm)

-endq <real> (2)
    largest q value (1/nm)

-qspacing <real> (0.01)
    spacing of q values (1/nm)

-binwidth <real> (0.1)
    Bin width (nm) for P(r)

-mc-coverage <real> (0.2)
    coverage of Monte Carlo (%)

-seed <int> (2023)
    random seed for Monte Carlo

-[no]norm (no)
    normalize scattering intensities

-[no]mc (yes)
    use Monte Carlo to scattering intensities

-scattering-type <enum> (sans)
    Scattering type: saxs, sans

SEE ALSO

gmx(1)

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