gmx sans¶
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