gmx-sans (1)

gmx sans [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]

         [-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]]
         [-prframe [<.xvg>]] [-sqframe [<.xvg>]] [-nice <int>]
         [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
         [-xvg <enum>] [-mode <enum>] [-mcover <real>] [-[no]pbc]
         [-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).

Parameters:

-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 and output files:

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)

    Run input file: tpr tpb tpa

-f [<.xtc/.trr/...>] (traj.xtc) (Input)

    Trajectory: xtc trr cpt trj gro g96 pdb tng

-n [<.ndx>] (index.ndx) (Input, Optional)

    Index file

-d [<.dat>] (nsfactor.dat) (Input, Optional)

    Generic data file

-pr [<.xvg>] (pr.xvg) (Output)

    xvgr/xmgr file

-sq [<.xvg>] (sq.xvg) (Output)

    xvgr/xmgr file

-prframe [<.xvg>] (prframe.xvg) (Output, Optional)

    xvgr/xmgr file

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

    xvgr/xmgr file

Other options:

-nice <int> (19)

    Set the nicelevel

-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)

    Time unit: fs, ps, ns, us, ms, s

-xvg <enum> (xmgrace)

    xvg plot formatting: xmgrace, xmgr, none

-mode <enum> (direct)

    Mode for sans spectra calculation: direct, mc

-mcover <real> (-1)

    Monte-Carlo coverage should be -1(default) or (0,1]

-[no]pbc (yes)

    Use periodic boundary conditions for computing distances

-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

gromacs(7)

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