Scroll to navigation

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:

Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
Input structure: tpr gro g96 pdb brk ent
Extra index groups

Options to specify output files:

scattering intensity as a function of q

Other options:

First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
Provide selections from files
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
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
Selection for Scattering calculation
smallest q value (1/nm)
largest q value (1/nm)
spacing of q values (1/nm)
Bin width (nm) for P(r)
coverage of Monte Carlo (%)
random seed for Monte Carlo
-[no]norm (no)
normalize scattering intensities
-[no]mc (yes)
use Monte Carlo to scattering intensities
Scattering type: saxs, sans

SEE ALSO

gmx(1)

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

COPYRIGHT

2024, GROMACS development team

August 29, 2024 2024.3