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

# g\_rms(1)

Calculate RMSDs with a reference structure and RMSD matrices

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

## NAME

gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices

## SYNOPSIS

gmx rms \[-s \[\<.tpr/.tpb/...\>\]\] \[-f \[\<.xtc/.trr/...\>\]\]\
         \[-f2 \[\<.xtc/.trr/...\>\]\] \[-n \[\<.ndx\>\]\] \[-o \[\<.xvg\>\]\]\
         \[-mir \[\<.xvg\>\]\] \[-a \[\<.xvg\>\]\] \[-dist \[\<.xvg\>\]\] \[-m \[\<.xpm\>\]\]\
         \[-bin \[\<.dat\>\]\] \[-bm \[\<.xpm\>\]\] \[-nice \<int\>\] \[-b \<time\>\]\
         \[-e \<time\>\] \[-dt \<time\>\] \[-tu \<enum\>\] \[-\[no\]w\] \[-xvg \<enum\>\]\
         \[-what \<enum\>\] \[-\[no\]pbc\] \[-fit \<enum\>\] \[-prev \<int\>\]\
         \[-\[no\]split\] \[-skip \<int\>\] \[-skip2 \<int\>\] \[-max \<real\>\]\
         \[-min \<real\>\] \[-bmax \<real\>\] \[-bmin \<real\>\] \[-\[no\]mw\]\
         \[-nlevels \<int\>\] \[-ng \<int\>\]

## DESCRIPTION

**gmx rms** compares two structures by computing the root mean square deviation (RMSD), the size-independent rho similarity parameter (**rho**) or the scaled rho (**rhosc**), see Maiorov & Crippen, Proteins **22**, 273 (1995). This is selected by **-what**.

Each structure from a trajectory (**-f**) is compared to a reference structure. The reference structure is taken from the structure file (**-s**).

With option **-mir** also a comparison with the mirror image of the reference structure is calculated. This is useful as a reference for 'significant' values, see Maiorov & Crippen, Proteins **22**, 273 (1995).

Option **-prev** produces the comparison with a previous frame the specified number of frames ago.

Option **-m** produces a matrix in **.xpm** format of comparison values of each structure in the trajectory with respect to each other structure. This file can be visualized with for instance **xv** and can be converted to postscript with **gmx xpm2ps**.

Option **-fit** controls the least-squares fitting of the structures on top of each other: complete fit (rotation and translation), translation only, or no fitting at all.

Option **-mw** controls whether mass weighting is done or not. If you select the option (default) and supply a valid **.tpr** file masses will be taken from there, otherwise the masses will be deduced from the **atommass.dat** file in **GMXLIB**. This is fine for proteins, but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned to unknown atoms. You can check whether this happend by turning on the **-debug** flag and inspecting the log file.

With **-f2**, the 'other structures' are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other.

Option **-bin** does a binary dump of the comparison matrix.

Option **-bm** produces a matrix of average bond angle deviations analogously to the **-m** option. Only bonds between atoms in the comparison group are considered.

## OPTIONS

Options to specify input and output files:

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

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

**-f2** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input, Optional)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

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

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

**-mir** *\[\<.xvg\>\] (rmsdmir.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-a** *\[\<.xvg\>\] (avgrp.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-dist** *\[\<.xvg\>\] (rmsd-dist.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-m** *\[\<.xpm\>\] (rmsd.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

**-bin** *\[\<.dat\>\] (rmsd.dat) (Output, Optional)*\
     Generic data file

**-bm** *\[\<.xpm\>\] (bond.xpm) (Output, Optional)*\
     X PixMap compatible matrix 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

**-what** *\<enum\> (rmsd)*\
     Structural difference measure: rmsd, rho, rhosc

**-\[no\]pbc**  *(yes)*\
     PBC check

**-fit** *\<enum\> (rot+trans)*\
     Fit to reference structure: rot+trans, translation, none

**-prev** *\<int\> (0)*\
     Compare with previous frame

**-\[no\]split**  *(no)*\
     Split graph where time is zero

**-skip** *\<int\> (1)*\
     Only write every nr-th frame to matrix

**-skip2** *\<int\> (1)*\
     Only write every nr-th frame to matrix

**-max** *\<real\> (-1)*\
     Maximum level in comparison matrix

**-min** *\<real\> (-1)*\
     Minimum level in comparison matrix

**-bmax** *\<real\> (-1)*\
     Maximum level in bond angle matrix

**-bmin** *\<real\> (-1)*\
     Minimum level in bond angle matrix

**-\[no\]mw**  *(yes)*\
     Use mass weighting for superposition

**-nlevels** *\<int\> (80)*\
     Number of levels in the matrices

**-ng** *\<int\> (1)*\
     Number of groups to compute RMS between

## SEE ALSO

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

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