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

# g\_mindist(1)

Calculate the minimum distance between two groups

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

## NAME

gmx-mindist - Calculate the minimum distance between two groups

## SYNOPSIS

gmx mindist \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
             \[-n \[\<.ndx\>\]\] \[-od \[\<.xvg\>\]\] \[-on \[\<.xvg\>\]\] \[-o \[\<.out\>\]\]\
             \[-ox \[\<.xtc/.trr/...\>\]\] \[-or \[\<.xvg\>\]\] \[-nice \<int\>\]\
             \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\] \[-tu \<enum\>\]\
             \[-\[no\]w\] \[-xvg \<enum\>\] \[-\[no\]matrix\] \[-\[no\]max\]\
             \[-d \<real\>\] \[-\[no\]group\] \[-\[no\]pi\] \[-\[no\]split\]\
             \[-ng \<int\>\] \[-\[no\]pbc\] \[-\[no\]respertime\]\
             \[-\[no\]printresname\]

## DESCRIPTION

**gmx mindist** computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the **-group** option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. With **-or**, minimum distances to each residue in the first group are determined and plotted as a function of residue number.

With option **-pi** the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors.

Also **gmx distance** calculates distances.

## 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, Optional)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

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

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

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

**-o** *\[\<.out\>\] (atm-pair.out) (Output, Optional)*\
     Generic output file

**-ox** *\[\<.xtc/.trr/...\>\] (mindist.xtc) (Output, Optional)*\
     Trajectory: xtc trr trj gro g96 pdb tng

**-or** *\[\<.xvg\>\] (mindistres.xvg) (Output, Optional)*\
     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

**-\[no\]matrix**  *(no)*\
     Calculate half a matrix of group-group distances

**-\[no\]max**  *(no)*\
     Calculate \*maximum\* distance instead of minimum

**-d** *\<real\> (0.6)*\
     Distance for contacts

**-\[no\]group**  *(no)*\
     Count contacts with multiple atoms in the first group as one

**-\[no\]pi**  *(no)*\
     Calculate minimum distance with periodic images

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

**-ng** *\<int\> (1)*\
     Number of secondary groups to compute distance to a central group

**-\[no\]pbc**  *(yes)*\
     Take periodic boundary conditions into account

**-\[no\]respertime**  *(no)*\
     When writing per-residue distances, write distance for each time point

**-\[no\]printresname**  *(no)*\
     Write residue names

## SEE ALSO

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

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