gmx sans

Main Table of Contents VERSION 5.0.7


gmx sans [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
         [-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]] [-prframe [<.xvg>]]
         [-sqframe [<.xvg>]] [-nice ] [-b 


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 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