| GMX-SANS(1) | GROMACS | GMX-SANS(1) |
NAME¶
gmx-sans - Compute small angle neutron scattering spectra
SYNOPSIS¶
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>]
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 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)
- Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
- Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
- Only use frame when t MOD dt = first time (default unit 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
SEE ALSO¶
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2022, GROMACS development team
| November 16, 2022 | 2022.4 |