gmx-saxs1
Compute small angle x-ray scattering spectra
Usage
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>]
Overview
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) |
Releases
5 releases since Debian 8 (Jessie); the text changed 4 times.