gmx-saxs(1) GROMACS Manual gmx-saxs(1)NAMEgmx-saxs - Compute small angle X-ray scattering spectra
SYNOPSIS
gmx saxs [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-d [<.dat>]] [-sq [<.xvg>]] [-nice <int>] [-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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-d [<.dat>] (sfactor.dat) (Input, Optional)
Generic data file
-sq [<.xvg>] (sq.xvg) (Output)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-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 when t MOD dt = first time (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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-saxs(1)
