1GMX-DYECOUPL(1)                     GROMACS                    GMX-DYECOUPL(1)
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NAME

6       gmx-dyecoupl - Extract dye dynamics from trajectories
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SYNOPSIS

9          gmx dyecoupl [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-ot [<.xvg>]]
10                       [-oe [<.xvg>]] [-o [<.dat>]] [-rhist [<.xvg>]]
11                       [-khist [<.xvg>]] [-b <time>] [-e <time>] [-tu <enum>]
12                       [-[no]w] [-xvg <enum>] [-[no]pbcdist] [-[no]norm]
13                       [-bins <int>] [-R0 <real>]
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DESCRIPTION

16       gmx dyecoupl extracts dye dynamics from trajectory files.  Currently, R
17       and kappa^2 between dyes  is  extracted  for  (F)RET  simulations  with
18       assumed  dipolar  coupling  as  in  the  Foerster equation.  It further
19       allows the calculation of R(t) and kappa^2(t), R and kappa^2 histograms
20       and  averages,  as well as the instantaneous FRET efficiency E(t) for a
21       specified Foerster radius R_0 (switch -R0).  The input dyes have to  be
22       whole  (see  res  and  mol pbc options in trjconv).  The dye transition
23       dipole moment has to be defined by at least a single atom pair, however
24       multiple  atom  pairs can be provided in the index file. The distance R
25       is calculated on the basis of the COMs of the given  atom  pairs.   The
26       -pbcdist  option  calculates  distances  to  the nearest periodic image
27       instead to the distance in the box. This works however only, for  peri‐
28       odic  boundaries in all 3 dimensions.  The -norm option (area-) normal‐
29       izes the histograms.
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OPTIONS

32       Options to specify input files:
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34       -f [<.xtc/.trr/…>] (traj.xtc)
35              Trajectory: xtc trr cpt gro g96 pdb tng
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37       -n [<.ndx>] (index.ndx)
38              Index file
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40       Options to specify output files:
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42       -ot [<.xvg>] (rkappa.xvg) (Optional)
43              xvgr/xmgr file
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45       -oe [<.xvg>] (insteff.xvg) (Optional)
46              xvgr/xmgr file
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48       -o [<.dat>] (rkappa.dat) (Optional)
49              Generic data file
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51       -rhist [<.xvg>] (rhist.xvg) (Optional)
52              xvgr/xmgr file
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54       -khist [<.xvg>] (khist.xvg) (Optional)
55              xvgr/xmgr file
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57       Other options:
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59       -b <time> (0)
60              Time of first frame to read from trajectory (default unit ps)
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62       -e <time> (0)
63              Time of last frame to read from trajectory (default unit ps)
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65       -tu <enum> (ps)
66              Unit for time values: fs, ps, ns, us, ms, s
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68       -[no]w (no)
69              View output .xvg, .xpm, .eps and .pdb files
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71       -xvg <enum> (xmgrace)
72              xvg plot formatting: xmgrace, xmgr, none
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74       -[no]pbcdist (no)
75              Distance R based on PBC
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77       -[no]norm (no)
78              Normalize histograms
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80       -bins <int> (50)
81              # of histogram bins
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83       -R0 <real> (-1)
84              Foerster radius including kappa^2=2/3 in nm
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SEE ALSO

87       gmx(1)
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89       More    information    about    GROMACS    is    available    at     <‐
90       http://www.gromacs.org/>.
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93       2020, GROMACS development team
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982019.6                           Feb 28, 2020                  GMX-DYECOUPL(1)
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