---
name: "g_morph_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-morph"
---

# g\_morph\_d(1)

Interpolate linearly between conformations

Part of [gmx-morph(1)](/gmx-morph/1.md).

## NAME

gmx-morph - Interpolate linearly between conformations

## SYNOPSIS

gmx morph \[-f1 \[\<.gro/.g96/...\>\]\] \[-f2 \[\<.gro/.g96/...\>\]\]\
           \[-o \[\<.xtc/.trr/...\>\]\] \[-or \[\<.xvg\>\]\] \[-n \[\<.ndx\>\]\]\
           \[-nice \<int\>\] \[-\[no\]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 and output files:

**-f1** *\[\<.gro/.g96/...\>\] (conf1.gro) (Input)*\
     Structure file: gro g96 pdb brk ent esp tpr tpb tpa

**-f2** *\[\<.gro/.g96/...\>\] (conf2.gro) (Input)*\
     Structure file: gro g96 pdb brk ent esp tpr tpb tpa

**-o** *\[\<.xtc/.trr/...\>\] (interm.xtc) (Output)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-or** *\[\<.xvg\>\] (rms-interm.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

Other options:

**-nice** *\<int\> (0)*\
     Set the nicelevel

**-\[no\]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

**[gromacs(7)](/gromacs/7.md)**

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