NAME

       g_sans - computes the small angle neutron scattering spectra

       VERSION 4.6.5

SYNOPSIS

       g_sans  -s  topol.tpr -f traj.xtc -n index.ndx -d nsfactor.dat -pr pr.xvg -sq sq.xvg -prframe prframe.xvg
       -sqframe sqframe.xvg -[no]h -[no]version -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

       This is simple tool to compute 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!

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input, Opt.
        Index file

       -d nsfactor.dat Input, Opt.
        Generic data file

       -pr pr.xvg Output
        xvgr/xmgr file

       -sq sq.xvg Output
        xvgr/xmgr file

       -prframe prframe.xvg Output, Opt.
        xvgr/xmgr file

       -sqframe sqframe.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -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 or  s

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -mode enum direct
        Mode for sans spectra calculation:  direct or  mc

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

       -[no]pbcyes
        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/>.

                                                 Mon 2 Dec 2013                                        g_sans(1)