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

# g\_rmsdist(1)

Calculate atom pair distances averaged with power -2, -3 or -6

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

## NAME

gmx-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6

## SYNOPSIS

gmx rmsdist \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
             \[-n \[\<.ndx\>\]\] \[-equiv \[\<.dat\>\]\] \[-o \[\<.xvg\>\]\]\
             \[-rms \[\<.xpm\>\]\] \[-scl \[\<.xpm\>\]\] \[-mean \[\<.xpm\>\]\]\
             \[-nmr3 \[\<.xpm\>\]\] \[-nmr6 \[\<.xpm\>\]\] \[-noe \[\<.dat\>\]\]\
             \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\]\
             \[-\[no\]w\] \[-xvg \<enum\>\] \[-nlevels \<int\>\] \[-max \<real\>\]\
             \[-\[no\]sumh\] \[-\[no\]pbc\]

## DESCRIPTION

**gmx rmsdist** computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by **gmx rms**. The reference structure is taken from the structure file. The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t.

**gmx rmsdist** can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 averaged distance below the maximum distance (**-max**, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named \*\[123\]). Additionally a list of equivalent atoms can be supplied (**-equiv**), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.:

**HB\* 3 SER  HB1 3 SER  HB2**

Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.

## 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

**-equiv** *\[\<.dat\>\] (equiv.dat) (Input, Optional)*\
     Generic data file

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

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

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

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

**-nmr3** *\[\<.xpm\>\] (nmr3.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

**-nmr6** *\[\<.xpm\>\] (nmr6.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

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

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

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

**-nlevels** *\<int\> (40)*\
     Discretize RMS in this number of levels

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

**-\[no\]sumh**  *(yes)*\
     Average distance over equivalent hydrogens

**-\[no\]pbc**  *(yes)*\
     Use periodic boundary conditions when computing distances

## SEE ALSO

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

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