1g_morph(1)                GROMACS suite, VERSION 4.5                g_morph(1)
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NAME

6       g_morph - linear interpolation of conformations
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8       VERSION 4.5
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SYNOPSIS

11       g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n
12       index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum  -ninterm  int
13       -first real -last real -[no]fit
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DESCRIPTION

16       g_morph does a linear interpolation of conformations in order to create
17       intermediates. Of course these are completely unphysical, but that  you
18       may try to justify yourself. Output is in the form of a generic trajec‐
19       tory. The number of intermediates can be controlled with  the  -ninterm
20       flag. The first and last flag correspond to the way of interpolating: 0
21       corresponds to input structure 1 while 1 corresponds to input structure
22       2.   If  you  specify  first  0 or last  1 extrapolation will be on the
23       path from input structure x1 to x2. In general the coordinates  of  the
24       intermediate x(i) out of N total intermidates correspond to:
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27       x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)
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30       Finally  the RMSD with respect to both input structures can be computed
31       if explicitly selected (-or option). In that case an index file may  be
32       read to select what group RMS is computed from.
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FILES

35       -f1 conf1.gro Input
36        Structure file: gro g96 pdb tpr etc.
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38       -f2 conf2.gro Input
39        Structure file: gro g96 pdb tpr etc.
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41       -o interm.xtc Output
42        Trajectory: xtc trr trj gro g96 pdb cpt
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44       -or rms-interm.xvg Output, Opt.
45        xvgr/xmgr file
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47       -n index.ndx Input, Opt.
48        Index file
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OTHER OPTIONS

52       -[no]hno
53        Print help info and quit
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55       -[no]versionno
56        Print version info and quit
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58       -nice int 0
59        Set the nicelevel
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61       -[no]wno
62        View output xvg, xpm, eps and pdb files
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64       -xvg enum xmgrace
65        xvg plot formatting:  xmgrace,  xmgr or  none
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67       -ninterm int 11
68        Number of intermediates
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70       -first real 0
71        Corresponds to first generated structure (0 is input x0, see above)
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73       -last real 1
74        Corresponds to last generated structure (1 is input x1, see above)
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76       -[no]fityes
77        Do  a  least  squares  fit of the second to the first structure before
78       interpolating
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SEE ALSO

82       gromacs(7)
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84       More  information  about  GROMACS  is  available  at   <http://www.gro‐
85       macs.org/>.
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89                                Thu 26 Aug 2010                     g_morph(1)
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