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gmx-sans(1)			GROMACS	Manual			   gmx-sans(1)

NAME
       gmx-sans	- Compute small	angle neutron scattering spectra

SYNOPSIS
       gmx sans	[-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
		[-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]]
		[-prframe [<.xvg>]] [-sqframe [<.xvg>]]	[-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
       gmx  sans  computes 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!

OPTIONS
       Options to specify input	and output files:

       -s [_.tpr/.tpb/..._] (topol.tpr)	(Input)
	   Run input file: tpr tpb tpa

       -f [_.xtc/.trr/..._] (traj.xtc) (Input)
	   Trajectory: xtc trr cpt trj gro g96 pdb tng

       -n [_.ndx_] (index.ndx) (Input, Optional)
	   Index file

       -d [_.dat_] (nsfactor.dat) (Input, Optional)
	   Generic data	file

       -pr [_.xvg_] (pr.xvg) (Output)
	   xvgr/xmgr file

       -sq [_.xvg_] (sq.xvg) (Output)
	   xvgr/xmgr file

       -prframe	[_.xvg_] (prframe.xvg) (Output,	Optional)
	   xvgr/xmgr file

       -sqframe	[_.xvg_] (sqframe.xvg) (Output,	Optional)
	   xvgr/xmgr file

       Other options:

       -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, 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
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro-
       macs.org/>.

VERSION	5.0.6							   gmx-sans(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO

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