table of contents
g_morph(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_morph(1) |
NAME¶
g_morph - linear interpolation of conformationsSYNOPSIS¶
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]fitDESCRIPTION¶
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:FILES¶
-f1 conf1.gro InputStructure file: gro g96 pdb tpr etc.
Structure file: gro g96 pdb tpr etc.
Trajectory: xtc trr trj gro g96 pdb cpt
xvgr/xmgr file
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Number of intermediates
Corresponds to first generated structure (0 is input x0, see above)
Corresponds to last generated structure (1 is input x1, see above)
Do a least squares fit of the second to the first structure before interpolating
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |