| 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¶
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2024, GROMACS development team
| January 30, 2024 | 2024 |