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)-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