gmx saxs-legacy#
Synopsis#
gmx saxs-legacy [-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-legacy
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)-s
[<.tpr/.gro/…>] (topol.tpr)-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)