Man page - gmx-scattering(1)
Packages contas this manual
- gmx-wham(1)
- gmx-trjcat(1)
- gmx-confrms(1)
- gmx_d(1)
- gmx-xpm2ps(1)
- gmx-make_edi(1)
- gmx-solvate(1)
- gmx-awh(1)
- gmx-help(1)
- gmx-hydorder(1)
- gmx-velacc(1)
- gmx-order(1)
- gmx-clustsize(1)
- gmx-densorder(1)
- gmx-msd(1)
- gmx-saxs-legacy(1)
- gmx-covar(1)
- gmx-tcaf(1)
- gmx-filter(1)
- gmx-rms(1)
- gmx-bundle(1)
- gmx-vanhove(1)
- gmx-enemat(1)
- gmx-rama(1)
- gmx-spatial(1)
- gmx-nmens(1)
- gmx-mdmat(1)
- gmx-rotmat(1)
- gmx(1)
- gmx-eneconv(1)
- gmx-h2order(1)
- gmx-current(1)
- gmx-genion(1)
- gmx-rmsdist(1)
- gmx-report-methods(1)
- gmx-distance(1)
- gmx-insert-molecules(1)
- demux(1)
- gmx-dielectric(1)
- gmx-sans-legacy(1)
- gmx-sigeps(1)
- gmx-genrestr(1)
- gmx-analyze(1)
- gmx-convert-tpr(1)
- gmx-potential(1)
- gmx-wheel(1)
- gmx-mk_angndx(1)
- gmx-x2top(1)
- gmx-genconf(1)
- gmx-mindist(1)
- gmx-dipoles(1)
- gmx-polystat(1)
- gmx-hbond-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-make_ndx(1)
- gmx-nonbonded-benchmark(1)
- gmx-sham(1)
- gmx-nmr(1)
- xplor2gmx(1)
- gmx-densmap(1)
- gmx-bar(1)
- gmx-trajectory(1)
- gmx-sasa(1)
- gmx-dos(1)
- gmx-principal(1)
- gmx-pme_error(1)
- gmx-hbond(1)
- gmx-dump(1)
- gmx-traj(1)
- gmx-freevolume(1)
- gmx-trjconv(1)
- gmx_mpi(1)
- gmx-density(1)
- gmx-pdb2gmx(1)
- gmx-spol(1)
- gmx-cluster(1)
- gmx-select(1)
- gmx-rmsf(1)
- gmx-angle(1)
- gmx-saltbr(1)
- gmx-scattering(1)
- gmx-energy(1)
- gmx-dyecoupl(1)
- gmx-disre(1)
- gmx-pairdist(1)
- gmx-extract-cluster(1)
- gmx-tune_pme(1)
- gmx-check(1)
- gmx-nmtraj(1)
- gmx-helix(1)
- gmx-trjorder(1)
- gmx-grompp(1)
- gmx-gangle(1)
- gmx-dssp(1)
- gmx-convert-trj(1)
- gmx-sorient(1)
- gmx-chi(1)
- gmx-anaeig(1)
- gmx-lie(1)
- gmx-helixorient(1)
- gmx-mdrun(1)
- gmx-editconf(1)
- gmx-rdf(1)
- gmx_mpi_d(1)
- gmx-rotacf(1)
- gmx-nmeig(1)
- gmx-gyrate(1)
Package: gromacs-data
apt-get install gromacs-data
apt-get install gromacs-data
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Manual
| 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
| May 12, 2025 | 2025.2 |