gmx scattering

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