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gmx-sans - Online in the Cloud

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This is the command gmx-sans that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-sans - Compute small angle neutron scattering spectra

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)
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)
Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum>
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

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