GMX-SANS-LEGACY(1) GROMACS GMX-SANS-LEGACY(1) 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 h5md -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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-SANS-LEGACY(1)
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