g_morph VERSION 3.3_beta_20050823

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

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.

-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

-[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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.