1 .TH g_morph 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_morph - linear interpolation of conformations
8 .BI "\-f1" " conf1.gro "
9 .BI "\-f2" " conf2.gro "
10 .BI "\-o" " interm.xtc "
11 .BI "\-or" " rms\-interm.xvg "
12 .BI "\-n" " index.ndx "
14 .BI "\-[no]version" ""
18 .BI "\-ninterm" " int "
19 .BI "\-first" " real "
23 \&g_morph does a linear interpolation of conformations in order to
24 \&create intermediates. Of course these are completely unphysical, but
25 \&that you may try to justify yourself. Output is in the form of a
26 \&generic trajectory. The number of intermediates can be controlled with
27 \&the \-ninterm flag. The first and last flag correspond to the way of
28 \&interpolating: 0 corresponds to input structure 1 while
29 \&1 corresponds to input structure 2.
30 \&If you specify first 0 or last 1 extrapolation will be
31 \&on the path from input structure x1 to x2. In general the coordinates
32 \&of the intermediate x(i) out of N total intermidates correspond to:
35 \&x(i) = x1 + (first+(i/(N\-1))*(last\-first))*(x2\-x1)
38 \&Finally the RMSD with respect to both input structures can be computed
39 \&if explicitly selected (\-or option). In that case an index file may be
40 \&read to select what group RMS is computed from.
42 .BI "\-f1" " conf1.gro"
44 Structure file: gro g96 pdb tpr etc.
46 .BI "\-f2" " conf2.gro"
48 Structure file: gro g96 pdb tpr etc.
50 .BI "\-o" " interm.xtc"
52 Trajectory: xtc trr trj gro g96 pdb cpt
54 .BI "\-or" " rms\-interm.xvg"
58 .BI "\-n" " index.ndx"
64 Print help info and quit
66 .BI "\-[no]version" "no "
67 Print version info and quit
69 .BI "\-nice" " int" " 0"
73 View output xvg, xpm, eps and pdb files
75 .BI "\-xvg" " enum" " xmgrace"
76 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
78 .BI "\-ninterm" " int" " 11"
79 Number of intermediates
81 .BI "\-first" " real" " 0 "
82 Corresponds to first generated structure (0 is input x0, see above)
84 .BI "\-last" " real" " 1 "
85 Corresponds to last generated structure (1 is input x1, see above)
87 .BI "\-[no]fit" "yes "
88 Do a least squares fit of the second to the first structure before interpolating
93 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.