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

# g\_principal(1)

Calculate principal axes of inertia for a group of atoms

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

## NAME

gmx-principal - Calculate principal axes of inertia for a group of atoms

## SYNOPSIS

gmx principal \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
              \[-n \[\<.ndx\>\]\] \[-a1 \[\<.xvg\>\]\] \[-a2 \[\<.xvg\>\]\]\
              \[-a3 \[\<.xvg\>\]\] \[-om \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\]\
              \[-e \<time\>\] \[-dt \<time\>\] \[-tu \<enum\>\] \[-\[no\]w\]\
              \[-xvg \<enum\>\] \[-\[no\]foo\]

## DESCRIPTION

**gmx principal** calculates the three principal axes of inertia for a group of atoms. NOTE: Old versions of Gromacs wrote the output data in a strange transposed way. As of Gromacs-5.0, the output file paxis1.dat contains the x/y/z components of the first (major) principal axis for each frame, and similarly for the middle and minor axes in paxis2.dat and paxis3.dat.

## OPTIONS

Options to specify input and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

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

**-a1** *\[\<.xvg\>\] (paxis1.xvg) (Output)*\
     xvgr/xmgr file

**-a2** *\[\<.xvg\>\] (paxis2.xvg) (Output)*\
     xvgr/xmgr file

**-a3** *\[\<.xvg\>\] (paxis3.xvg) (Output)*\
     xvgr/xmgr file

**-om** *\[\<.xvg\>\] (moi.xvg) (Output)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-b** *\<time\> (0)*\
     First frame (ps) to read from trajectory

**-e** *\<time\> (0)*\
     Last frame (ps) to read from trajectory

**-dt** *\<time\> (0)*\
     Only use frame when t MOD dt = first time (ps)

**-tu** *\<enum\> (ps)*\
     Time unit: fs, ps, ns, us, ms, s

**-\[no\]w**  *(no)*\
     View output **.xvg**, **.xpm**, **.eps** and **.pdb** files

**-xvg** *\<enum\> (xmgrace)*\
     xvg plot formatting: xmgrace, xmgr, none

**-\[no\]foo**  *(no)*\
     Dummy option to avoid empty array

## SEE ALSO

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

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