.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_morph - linear interpolation of conformations 

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_morph\fP
.BI "\-f1" " conf1.gro "
.BI "\-f2" " conf2.gro "
.BI "\-o" " interm.xtc "
.BI "\-or" " rms\-interm.xvg "
.BI "\-n" " index.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-ninterm" " int "
.BI "\-first" " real "
.BI "\-last" " real "
.BI "\-[no]fit" ""
.SH DESCRIPTION
\&\fB g_morph\fR 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 \fB \-ninterm\fR 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 \fB \-first\fR  0 or \fB \-last\fR  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 (\fB \-or\fR option). In that case, an index file may be
\&read to select the group from which the RMS is computed.
.SH FILES
.BI "\-f1" " conf1.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-f2" " conf2.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " interm.xtc" 
.B Output
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-or" " rms\-interm.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-ninterm"  " int" " 11" 
 Number of intermediates

.BI "\-first"  " real" " 0     " 
 Corresponds to first generated structure (0 is input x0, see above)

.BI "\-last"  " real" " 1     " 
 Corresponds to last generated structure (1 is input x1, see above)

.BI "\-[no]fit"  "yes   "
 Do a least squares fit of the second to the first structure before interpolating

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.