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

       2025, GROMACS development team

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

gmxsans-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!

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

       Options to specify input files:

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

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-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

gmx(1)

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

          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>]