g_morph(1)
NAME
g_morph - linear interpolation of conformations
SYNOPSIS
g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -nice int -[no]w -[no]xvgr -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 strucutre
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 what group RMS is computed from.
FILES
- -f1 conf1.gro Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
- -f2 conf2.gro Input
Generic structure: gro g96 pdb tpr tpb tpa xml - -o interm.xtc Output
Generic trajectory: xtc trr trj gro g96 pdb - -or rms-interm.xvg Output, Opt. xvgr/xmgr file
- -n index.ndx Input, Opt.
Index file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 0
Set the nicelevel - -[no]w no
View output xvg, xpm, eps and pdb files - -[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the - xmgrace program
- -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]fit yes
Do a least squares fit of the second to the first structure before - interpolating
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.