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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:

Portable xdr run input file
Trajectory: xtc trr cpt gro g96 pdb tng
Index file
Generic data file

Options to specify output files:

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
xvg plot formatting: xmgrace, xmgr, none
[HIDDEN]Binwidth (nm)
Mode for sans spectra calculation: direct, mc
Monte-Carlo coverage should be -1(default) or (0,1]
[HIDDEN]Method for sans spectra calculation: debye, fft
-[no]pbc (yes)
Use periodic boundary conditions for computing distances
[HIDDEN]Grid spacing (in nm) for FFTs
Starting q (1/nm)
Ending q (1/nm)
Stepping in q (1/nm)
Random seed for Monte-Carlo



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2022, GROMACS development team

June 16, 2022 2022.2