Man page - gmx-dyecoupl(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
- gmx-genrestr(1)
- gmx-bar(1)
- gmx-lie(1)
- gmx-filter(1)
- gmx-scattering(1)
- gmx-anaeig(1)
- gmx-covar(1)
- gmx_d(1)
- gmx-genconf(1)
- gmx-mdrun(1)
- gmx-velacc(1)
- gmx-tcaf(1)
- gmx-insert-molecules(1)
- gmx-bundle(1)
- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
- gmx-confrms(1)
- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
- gmx-current(1)
- gmx-freevolume(1)
- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
- gmx-gyrate(1)
- gmx-solvate(1)
- gmx-densmap(1)
- gmx-rotacf(1)
- gmx-helix(1)
- gmx_mpi(1)
- gmx-convert-tpr(1)
- gmx-convert-trj(1)
- gmx-polystat(1)
- gmx-angle(1)
- gmx-xpm2ps(1)
- gmx-pdb2gmx(1)
- gmx-sasa(1)
- gmx-x2top(1)
- gmx-trjcat(1)
- gmx-h2order(1)
- gmx-nmr(1)
- gmx-dump(1)
- gmx-spol(1)
- gmx-distance(1)
- gmx-clustsize(1)
- gmx-rama(1)
- gmx-chi(1)
- gmx-pme_error(1)
- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
- gmx-tune_pme(1)
- gmx-grompp(1)
- gmx-make_edi(1)
- gmx-trajectory(1)
- gmx-dipoles(1)
- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
- gmx-analyze(1)
- demux(1)
- gmx-disre(1)
- gmx-saxs-legacy(1)
- gmx-sigeps(1)
- gmx-mdmat(1)
- xplor2gmx(1)
- gmx-check(1)
- gmx-vanhove(1)
- gmx-dssp(1)
- gmx-densorder(1)
- gmx-principal(1)
- gmx-mindist(1)
- gmx-spatial(1)
- gmx-wham(1)
- gmx-rmsf(1)
- gmx-dos(1)
- gmx-mk_angndx(1)
- gmx-nmens(1)
- gmx-dielectric(1)
- gmx-sorient(1)
- gmx-help(1)
- gmx-hbond-legacy(1)
- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-DYECOUPL
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-dyecoupl - Extract dye dynamics from trajectories
SYNOPSIS
gmx dyecoupl
[
-f
[<.xtc/.trr/...>]
] [
-n
[<.ndx>]
] [
-ot
[<.xvg>]
]
[
-oe
[<.xvg>]
] [
-o
[<.dat>]
] [
-rhist
[<.xvg>]
]
[
-khist
[<.xvg>]
] [
-b
<time>
] [
-e
<time>
]
[
-tu
<enum>
]
[
-[no]w
] [
-xvg
<enum>
]
[
-[no]pbcdist
] [
-[no]norm
]
[
-bins
<int>
] [
-R0
<real>
]
DESCRIPTION
gmx dyecoupl extracts dye dynamics from trajectory files. Currently, R and kappaˆ2 between dyes is extracted for (F)RET simulations with assumed dipolar coupling as in the Foerster equation. It further allows the calculation of R(t) and kappaˆ2(t), R and kappaˆ2 histograms and averages, as well as the instantaneous FRET efficiency E(t) for a specified Foerster radius R_0 (switch -R0 ). The input dyes have to be whole (see res and mol pbc options in trjconv ). The dye transition dipole moment has to be defined by at least a single atom pair, however multiple atom pairs can be provided in the index file. The distance R is calculated on the basis of the COMs of the given atom pairs. The -pbcdist option calculates distances to the nearest periodic image instead to the distance in the box. This works however only, for periodic boundaries in all 3 dimensions. The -norm option (area-) normalizes the histograms.
OPTIONS
Options to
specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-n [<.ndx>] (index.ndx)
Index file
Options to
specify output files:
-ot [<.xvg>] (rkappa.xvg) (Optional)
xvgr/xmgr file
-oe [<.xvg>] (insteff.xvg) (Optional)
xvgr/xmgr file
-o [<.dat>] (rkappa.dat) (Optional)
Generic data file
-rhist [<.xvg>] (rhist.xvg) (Optional)
xvgr/xmgr file
-khist [<.xvg>] (khist.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)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg , .xpm , .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]pbcdist (no)
Distance R based on PBC
-[no]norm (no)
Normalize histograms
-bins <int> (50)
# of histogram bins
-R0 <real> (-1)
Foerster radius including kappaˆ2=2/3 in nm
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team