NAME

       gmx-sans-legacy - Compute small angle neutron scattering spectra

SYNOPSIS

          gmx sans-legacy [-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>]
                       [-mode <enum>] [-mcover <real>] [-[no]pbc]
                       [-startq <real>] [-endq <real>] [-qstep <real>]
                       [-seed <int>]

DESCRIPTION

       gmx  sans-legacy  computes  SANS  spectra using Debye formula.  It currently uses topology file (since it
       need to assign 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 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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu <enum> (ps)
              Unit for time values: 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

       gmx(1)

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

COPYRIGHT

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                GMX-SANS-LEGACY(1)