g_morph (1) - Linux Manuals
g_morph: linear interpolation of conformations
NAMEg_morph - linear interpolation of conformations
SYNOPSISg_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
DESCRIPTIONg_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
-nice int 0
-ninterm int 11
-first real 0
-last real 1
More information about GROMACS is available at <http://www.gromacs.org/>.