gmx-dyecoupl man page
gmx-dyecoupl ā Extract dye dynamics from trajectories gmx dyecoupl extracts dye dynamics from trajectory files. Currently, R and kappa^2 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 kappa^2(t), R and kappa^2 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 to specify input files: Trajectory: xtc trr cpt gro g96 pdb tng Index file Options to specify output files: xvgr/xmgr file xvgr/xmgr file Generic data file xvgr/xmgr file xvgr/xmgr file Other options: Time of first frame to read from trajectory (default unit ps) Time of last frame to read from trajectory (default unit ps) Unit for time values: fs, ps, ns, us, ms, s View output .xvg, .xpm, .eps and .pdb files xvg plot formatting: xmgrace, xmgr, none Distance R based on PBC Normalize histograms # of histogram bins Foerster radius including kappa^2=2/3 in nm More information about GROMACS is available at <http://www.gromacs.org/>. 2019, GROMACS development teamSynopsis
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
Options
See Also
Copyright
Referenced By