---
name: "gmx-morph"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2019.1-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-morph"
---

# gmx-morph(1)

Interpolate linearly between conformations

## NAME

gmx-morph - Interpolate linearly between conformations

## SYNOPSIS

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

## DESCRIPTION

**gmx 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 x\_1 to x\_2. In general, the coordinates** **of the intermediate x(i) out of N total intermediates correspond to:**

**x(i) = x\_1 + (first+(i/(N-1))\*(last-first))\*(x\_2-x\_1)**

**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.**

## OPTIONS

**Options to specify input files:**

- **-f1 \[\<.gro/.g96/…\>\] (conf1.gro)**

  **Structure file: gro g96 pdb brk ent esp tpr**

- **-f2 \[\<.gro/.g96/…\>\] (conf2.gro)**

  **Structure file: gro g96 pdb brk ent esp tpr**

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  **Index file**

**Options to specify output files:**

- **-o \[\<.xtc/.trr/…\>\] (interm.xtc)**

  **Trajectory: xtc trr cpt gro g96 pdb tng**

- **-or \[\<.xvg\>\] (rms-interm.xvg) (Optional)**

  **xvgr/xmgr file**

**Other options:**

- **-\[no\]w (no)**

  **View output .xvg, .xpm, .eps and .pdb files**

- **-xvg \<enum\> (xmgrace)**

  **xvg plot formatting: xmgrace, xmgr, none**

- **-ninterm \<int\> (11)**

  **Number of intermediates**

- **-first \<real\> (0)**

  **Corresponds to first generated structure (0 is input x\_1, see above)**

- **-last \<real\> (1)**

  **Corresponds to last generated structure (1 is input x\_2, see above)**

- **-\[no\]fit (yes)**

  **Do a least squares fit of the second to the first structure before interpolating**

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

**More information about GROMACS is available at \<***http://www.gromacs.org/***\>.**

## COPYRIGHT

**2019, GROMACS development team**