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>] [-nt <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
-nt <int> (96): Number of threads to start