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gmx-sans(1)                     GROMACS Manual                     gmx-sans(1)

NAME
       gmx-sans - Compute small angle neutron scattering spectra

SYNOPSIS
       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>]

DESCRIPTION
       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
       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

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at
       <http://www.gromacs.org/>.

VERSION 5.0.6                                                      gmx-sans(1)