.TH gmx-sans 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-sans \- Compute small angle neutron scattering spectra

.SH 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>]

.SH DESCRIPTION
\fBgmx sans\fR computes SANS spectra using Debye formula. It currently uses topology file (since it need to assigne element for each atom).

Parameters:

\fB\-pr\fR Computes normalized g(r) function averaged over trajectory

\fB\-prframe\fR Computes normalized g(r) function for each frame

\fB\-sq\fR Computes SANS intensity curve averaged over trajectory

\fB\-sqframe\fR Computes SANS intensity curve for each frame

\fB\-startq\fR Starting q value in nm

\fB\-endq\fR Ending q value in nm

\fB\-qstep\fR 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!

.SH OPTIONS
Options to specify input and output files:

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Run input file: tpr tpb tpa

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-d" " [<.dat>] (nsfactor.dat) (Input, Optional)"
    Generic data file

.BI "\-pr" " [<.xvg>] (pr.xvg) (Output)"
    xvgr/xmgr file

.BI "\-sq" " [<.xvg>] (sq.xvg) (Output)"
    xvgr/xmgr file

.BI "\-prframe" " [<.xvg>] (prframe.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-sqframe" " [<.xvg>] (sqframe.xvg) (Output, Optional)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-tu" " <enum> (ps)"
    Time unit: fs, ps, ns, us, ms, s

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-mode" " <enum> (direct)"
    Mode for sans spectra calculation: direct, mc

.BI "\-mcover" " <real> (-1)"
    Monte\-Carlo coverage should be \-1(default) or (0,1]

.BI "\-[no]pbc" "  (yes)"
    Use periodic boundary conditions for computing distances

.BI "\-startq" " <real> (0)"
    Starting q (1/nm)

.BI "\-endq" " <real> (2)"
    Ending q (1/nm)

.BI "\-qstep" " <real> (0.01)"
    Stepping in q (1/nm)

.BI "\-seed" " <int> (0)"
    Random seed for Monte\-Carlo


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.