1GMX-SANS(1)                         GROMACS                        GMX-SANS(1)
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NAME

6       gmx-sans - Compute small angle neutron scattering spectra
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SYNOPSIS

9          gmx sans [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
10                   [-d [<.dat>]] [-pr [<.xvg>]] [-sq [<.xvg>]]
11                   [-prframe [<.xvg>]] [-sqframe [<.xvg>]] [-b <time>]
12                   [-e <time>] [-dt <time>] [-tu <enum>] [-xvg <enum>]
13                   [-bin <real>] [-mode <enum>] [-mcover <real>]
14                   [-method <enum>] [-[no]pbc] [-grid <real>] [-startq <real>]
15                   [-endq <real>] [-qstep <real>] [-seed <int>]
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DESCRIPTION

18       gmx  sans computes SANS spectra using Debye formula.  It currently uses
19       topology file (since it need to assigne element for each atom).
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21       Parameters:
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23       -pr Computes normalized g(r) function averaged over trajectory
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25       -prframe Computes normalized g(r) function for each frame
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27       -sq Computes SANS intensity curve averaged over trajectory
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29       -sqframe Computes SANS intensity curve for each frame
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31       -startq Starting q value in nm
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33       -endq Ending q value in nm
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35       -qstep Stepping in q space
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37       Note: When using Debye direct method computational  cost  increases  as
38       1/2 * N * (N - 1) where N is atom number in group of interest.
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40       WARNING:  If  sq  or pr specified this tool can produce large number of
41       files! Up to two times larger than number of frames!
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OPTIONS

44       Options to specify input files:
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46       -s [<.tpr>] (topol.tpr)
47              Portable xdr run input file
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49       -f [<.xtc/.trr/…>] (traj.xtc)
50              Trajectory: xtc trr cpt gro g96 pdb tng
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52       -n [<.ndx>] (index.ndx) (Optional)
53              Index file
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55       -d [<.dat>] (nsfactor.dat) (Optional)
56              Generic data file
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58       Options to specify output files:
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60       -pr [<.xvg>] (pr.xvg)
61              xvgr/xmgr file
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63       -sq [<.xvg>] (sq.xvg)
64              xvgr/xmgr file
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66       -prframe [<.xvg>] (prframe.xvg) (Optional)
67              xvgr/xmgr file
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69       -sqframe [<.xvg>] (sqframe.xvg) (Optional)
70              xvgr/xmgr file
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72       Other options:
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74       -b <time> (0)
75              Time of first frame to read from trajectory (default unit ps)
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77       -e <time> (0)
78              Time of last frame to read from trajectory (default unit ps)
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80       -dt <time> (0)
81              Only use frame when t MOD dt = first time (default unit ps)
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83       -tu <enum> (ps)
84              Unit for time values: fs, ps, ns, us, ms, s
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86       -xvg <enum> (xmgrace)
87              xvg plot formatting: xmgrace, xmgr, none
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89       -bin <real> (0.2)
90              [HIDDEN]Binwidth (nm)
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92       -mode <enum> (direct)
93              Mode for sans spectra calculation: direct, mc
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95       -mcover <real> (-1)
96              Monte-Carlo coverage should be -1(default) or (0,1]
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98       -method <enum> (debye)
99              [HIDDEN]Method for sans spectra calculation: debye, fft
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101       -[no]pbc (yes)
102              Use periodic boundary conditions for computing distances
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104       -grid <real> (0.05)
105              [HIDDEN]Grid spacing (in nm) for FFTs
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107       -startq <real> (0)
108              Starting q (1/nm)
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110       -endq <real> (2)
111              Ending q (1/nm)
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113       -qstep <real> (0.01)
114              Stepping in q (1/nm)
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116       -seed <int> (0)
117              Random seed for Monte-Carlo
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SEE ALSO

120       gmx(1)
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122       More    information    about    GROMACS    is    available    at     <‐
123       http://www.gromacs.org/>.
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126       2019, GROMACS development team
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1312019.4                           Oct 02, 2019                      GMX-SANS(1)
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