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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 cur-
       rently 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)

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