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gmx-saxs - Online in the Cloud

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This is the command gmx-saxs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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)
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>
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)

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