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gmx-sans - Compute small angle neutron scattering spectra



gmx-sans - Compute small angle neutron scattering spectra


gmx sans [ -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>]
         [ -bin <real>] [-mode <enum>] [-mcover <real>]
         [ -method <enum>] [-[no]pbc] [-grid <real>] [-startq <real>]
         [ -endq <real>] [-qstep <real>] [-seed <int>]


gmx sans computes SANS spectra using Debye formula. It currently uses topology file (since it need to assigne element for each atom).
-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 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)
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)
Unit for time values: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-bin <real> (0.2)
[HIDDEN]Binwidth (nm)
-mode <enum> (direct)
Mode for sans spectra calculation: direct, mc
-mcover <real> (-1)
Monte-Carlo coverage should be -1(default) or (0,1]
-method <enum> (debye)
[HIDDEN]Method for sans spectra calculation: debye, fft
-[no]pbc (yes)
Use periodic boundary conditions for computing distances
-grid <real> (0.05)
[HIDDEN]Grid spacing (in nm) for FFTs
-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


More information about GROMACS is available at <>. 2017, GROMACS development team
September 15, 2017 2016.4