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gmx-sans - Compute small angle neutron scattering spectra


gmx sans [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]]
[-prframe [<.xvg>]] [-sqframe [<.xvg>]] [-b <time>]
[-e <time>] [-dt <time>] [-tu <enum>] [-xvg <enum>]
[-bin <real>] [-mode <enum>] [-mcover <real>]
[-method <enum>] [-[no]pbc] [-grid <real>] [-startq <real>]
[-endq <real>] [-qstep <real>] [-seed <int>]


gmx sans computes SANS spectra using Debye formula. It currently uses topology file
(since it need to assigne element for each atom).


-pr Computes normalized g(r) function averaged over trajectory

-prframe Computes normalized g(r) function for each frame

-sq Computes SANS intensity curve averaged over trajectory

-sqframe Computes SANS intensity curve for each frame

-startq Starting q value in nm

-endq Ending q value in nm

-qstep Stepping in q space

Note: When using Debye direct method computational cost increases as 1/2 * N * (N - 1)
where N is atom number in group of interest.

WARNING: If sq or pr specified this tool can produce large number of files! Up to two
times larger than number of frames!


Options to specify input files:

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx) (Optional)
Index file

-d [<.dat>] (nsfactor.dat) (Optional)
Generic data file

Options to specify output files:

-pr [<.xvg>] (pr.xvg)
xvgr/xmgr file

-sq [<.xvg>] (sq.xvg)
xvgr/xmgr file

-prframe [<.xvg>] (prframe.xvg) (Optional)
xvgr/xmgr file

-sqframe [<.xvg>] (sqframe.xvg) (Optional)
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)

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-bin <real> (0.2)
[HIDDEN]Binwidth (nm)

-mode <enum> (direct)
Mode for sans spectra calculation: direct, mc

-mcover <real> (-1)
Monte-Carlo coverage should be -1(default) or (0,1]

-method <enum> (debye)
[HIDDEN]Method for sans spectra calculation: debye, fft

-[no]pbc (yes)
Use periodic boundary conditions for computing distances

-grid <real> (0.05)
[HIDDEN]Grid spacing (in nm) for FFTs

-startq <real> (0)
Starting q (1/nm)

-endq <real> (2)
Ending q (1/nm)

-qstep <real> (0.01)
Stepping in q (1/nm)

-seed <int> (0)
Random seed for Monte-Carlo

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