gmx-sans1
Compute small angle neutron scattering spectra
Usage
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>]
Overview
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 |
Releases
5 releases since Debian 8 (Jessie); the text changed 4 times.