g_sans(1)

NAME
g_sans - computes the small angle neutron scattering spectra VERSION 4.6.1

SYNOPSIS
g_sans -s topol.tpr -f traj.xtc -n index.ndx -d nsfactor.dat -pr pr.xvg -sq sq.xvg -prframe prframe.xvg -sqframe sqframe.xvg -[no]h -[no]version -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
This is simple tool to compute 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!

FILES
-s topol.tpr Input
 Run input file: tpr tpb tpa -f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt.
 Index file -d nsfactor.dat Input, Opt.
 Generic data file -pr pr.xvg Output
 xvgr/xmgr file -sq sq.xvg Output
 xvgr/xmgr file -prframe prframe.xvg Output, Opt.
 xvgr/xmgr file -sqframe sqframe.xvg Output, Opt.
 xvgr/xmgr file

OTHER OPTIONS
-[no]hno
 Print help info and quit -[no]versionno
 Print version info and quit -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 or s -xvg enum xmgrace
 xvg plot formatting: xmgrace, xmgr or none -mode enum direct
 Mode for sans spectra calculation: direct or mc -mcover real -1
 Monte-Carlo coverage should be -1(default) or (0,1] -[no]pbcyes
 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.gromacs.org/>.