NAME
gmx-saxs - Compute small angle X-ray scattering spectra
SYNOPSIS
gmx saxs
[-f [<.xtc/.trr/...>]]
[-s [<.tpr/.gro/...>]]
[-n [<.ndx>]]
[-d [<.dat>]] [-sq
[<.xvg>]] [-b
<time>] [-e
<time>]
[-dt <time>] [-xvg
<enum>] [-ng
<int>] [-startq
<real>]
[-endq <real>]
[-energy <real>]
DESCRIPTION
gmx saxs calculates SAXS structure factors for given index groups based on Cromer's method. Both topology and trajectory files are required.
OPTIONS
Options to
specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
-d [<.dat>] (sfactor.dat) (Optional)
Generic data file
Options to
specify output files:
-sq [<.xvg>] (sq.xvg)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-ng <int> (1)
Number of groups to compute SAXS
-startq <real> (0)
Starting q (1/nm)
-endq <real> (60)
Ending q (1/nm)
-energy <real> (12)
Energy of the incoming X-ray (keV)
SEE ALSO
More information about GROMACS is available at <- http://www.gromacs.org/>.
COPYRIGHT
2020, GROMACS development team