NAME
g_morph - linear interpolation of conformations
VERSION 4.0.1
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
Structure file: gro g96 pdb tpr tpb tpa
-f2 conf2.gro Input
Structure file: gro g96 pdb tpr tpb tpa
-o interm.xtc Output
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]hno
Print help info and quit
-nice int 0
Set the nicelevel
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
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]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/>.
Thu 16 Oct 2008 g_morph(1)