NAME¶

gmx-morph - Interpolate linearly between conformations

SYNOPSIS¶

gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]]
[-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-n [<.ndx>]]
[-nice <int>] [-[no]w] [-xvg <enum>] [-ninterm <int>]
[-first <real>] [-last <real>] [-[no]fit]

DESCRIPTION¶

gmx morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to justify yourself. Output is in the form of a generic trajectory. The number of intermediates can be controlled with the -ninterm flag. The first and last flag correspond to the way of interpolating: 0 corresponds to input structure 1 while 1 corresponds to input structure 2. If you specify -first 0 or -last 1 extrapolation will be on the path from input structure x_1 to x_2. In general, the coordinates of the intermediate x(i) out of N total intermediates correspond to: x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1) Finally the RMSD with respect to both input structures can be computed if explicitly selected ( -or option). In that case, an index file may be read to select the group from which the RMS is computed.

OPTIONS¶

Options to specify input and output files: -f1 [<.gro/.g96/...>] (conf1.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa -f2 [<.gro/.g96/...>] (conf2.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa -o [<.xtc/.trr/...>] (interm.xtc) (Output)
Trajectory: xtc trr cpt trj gro g96 pdb tng -or [<.xvg>] (rms-interm.xvg) (Output, Optional)
xvgr/xmgr file -n [<.ndx>] (index.ndx) (Input, Optional)
Index file Other options: -nice <int> (0)
Set the nicelevel -[no]w (no)
View output .xvg, .xpm, .eps and .pdb files -xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none -ninterm <int> (11)
Number of intermediates -first <real> (0)
Corresponds to first generated structure (0 is input x_1, see above) -last <real> (1)
Corresponds to last generated structure (1 is input x_2, see above) -[no]fit (yes)
Do a least squares fit of the second to the first structure before interpolating

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.