gmx saxs¶
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)