NAME¶

g_morph - linear interpolation of conformations VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm int -first real -last real -[no]fit

DESCRIPTION¶

g_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 x1 to x2. In general, the coordinates of the intermediate x(i) out of N total intermidates correspond to: x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1) 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.

FILES¶

-f1 conf1.gro Input
Structure file: gro g96 pdb tpr etc. -f2 conf2.gro Input
Structure file: gro g96 pdb tpr etc. -o interm.xtc Output
Trajectory: xtc trr trj gro g96 pdb cpt -or rms-interm.xvg Output, Opt.
xvgr/xmgr file -n index.ndx Input, Opt.
Index file

OTHER OPTIONS¶

-[no]hno
Print help info and quit -[no]versionno
Print version info and quit -nice int 0
Set the nicelevel -[no]wno
View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -ninterm int 11
Number of intermediates -first real 0
Corresponds to first generated structure (0 is input x0, see above) -last real 1
Corresponds to last generated structure (1 is input x1, see above) -[no]fityes
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/>.