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GMX-SCATTERING(1) GROMACS 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 -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 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-SCATTERING(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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