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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                 GMX-SCATTERING(1)

gmxscattering 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 gmxsans-legacy or gmxsaxs-legacy.

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

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)(Optional)
              Input trajectory or single configuration: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Input structure: tprgrog96pdb 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

gmx(1)

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

          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>]