1GMX-MORPH(1)                        GROMACS                       GMX-MORPH(1)
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NAME

6       gmx-morph - Interpolate linearly between conformations
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SYNOPSIS

9          gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]] [-n [<.ndx>]]
10                    [-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-[no]w]
11                    [-xvg <enum>] [-ninterm <int>] [-first <real>]
12                    [-last <real>] [-[no]fit]
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DESCRIPTION

15       gmx morph does a linear interpolation of conformations in order to cre‐
16       ate intermediates. Of course these are completely unphysical, but  that
17       you  may  try  to  justify yourself. Output is in the form of a generic
18       trajectory. The number of intermediates  can  be  controlled  with  the
19       -ninterm  flag. The first and last flag correspond to the way of inter‐
20       polating: 0 corresponds to input structure 1  while  1  corresponds  to
21       input  structure  2.  If you specify -first < 0 or -last > 1 extrapola‐
22       tion will be on the path from input structure x_1 to x_2.  In  general,
23       the  coordinates  of the intermediate x(i) out of N total intermediates
24       correspond to:
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26       x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)
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28       Finally the RMSD with respect to both input structures can be  computed
29       if explicitly selected (-or option). In that case, an index file may be
30       read to select the group from which the RMS is computed.
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OPTIONS

33       Options to specify input files:
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35       -f1 [<.gro/.g96/…>] (conf1.gro)
36              Structure file: gro g96 pdb brk ent esp tpr
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38       -f2 [<.gro/.g96/…>] (conf2.gro)
39              Structure file: gro g96 pdb brk ent esp tpr
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41       -n [<.ndx>] (index.ndx) (Optional)
42              Index file
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44       Options to specify output files:
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46       -o [<.xtc/.trr/…>] (interm.xtc)
47              Trajectory: xtc trr cpt gro g96 pdb tng
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49       -or [<.xvg>] (rms-interm.xvg) (Optional)
50              xvgr/xmgr file
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52       Other options:
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54       -[no]w (no)
55              View output .xvg, .xpm, .eps and .pdb files
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57       -xvg <enum> (xmgrace)
58              xvg plot formatting: xmgrace, xmgr, none
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60       -ninterm <int> (11)
61              Number of intermediates
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63       -first <real> (0)
64              Corresponds to first generated structure (0 is  input  x_1,  see
65              above)
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67       -last <real> (1)
68              Corresponds  to  last  generated  structure (1 is input x_2, see
69              above)
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71       -[no]fit (yes)
72              Do a least squares fit of the  second  to  the  first  structure
73              before interpolating
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SEE ALSO

76       gmx(1)
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78       More     information    about    GROMACS    is    available    at    <‐
79       http://www.gromacs.org/>.
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82       2019, GROMACS development team
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872018.7                           May 29, 2019                     GMX-MORPH(1)
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