Synopsis
gmx sans [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]] [-prframe [<.xvg>]]
[-sqframe [<.xvg>]] [-nice ] [-b
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 and output files:
- -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
-
Run input file: tpr tpb tpa
- -f [<.xtc/.trr/...>] (traj.xtc) (Input)
-
Trajectory: xtc trr cpt trj gro g96 pdb tng
- -n [<.ndx>] (index.ndx) (Input, Optional)
-
Index file
- -d [<.dat>] (nsfactor.dat) (Input, Optional)
-
Generic data file
- -pr [<.xvg>] (pr.xvg) (Output)
-
xvgr/xmgr file
- -sq [<.xvg>] (sq.xvg) (Output)
-
xvgr/xmgr file
- -prframe [<.xvg>] (prframe.xvg) (Output, Optional)
-
xvgr/xmgr file
- -sqframe [<.xvg>] (sqframe.xvg) (Output, Optional)
-
xvgr/xmgr file
Other options:
- -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, s
- -xvg <enum> (xmgrace)
-
xvg plot formatting: xmgrace, xmgr, none
- -mode <enum> (direct)
-
Mode for sans spectra calculation: direct, mc
- -mcover <real> (-1)
-
Monte-Carlo coverage should be -1(default) or (0,1]
- -[no]pbc (yes)
-
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
