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

       -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)

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

COPYRIGHT

       2024, GROMACS development team

2024.2                                            May 10, 2024                                 GMX-SCATTERING(1)