debian man page for g_morph

g_morph(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_morph(1)

NAME
       g_morph - linear interpolation of conformations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       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]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 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:

       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 the group from which the RMS is computed.

FILES
       -f1 conf1.gro Input
	Structure file: gro g96 pdb tpr etc.

       -f2 conf2.gro Input
	Structure file: gro g96 pdb tpr etc.

       -o interm.xtc Output
	Trajectory: xtc trr trj gro g96 pdb cpt

       -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

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -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/>.

								  Mon 4 Apr 2011							g_morph(1)