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Measuring Distances

Introduction

GROMACS has a few commands that can calculate the distance between atoms or groups of atoms:

gmx distance calculates distances between fixed pairs of atoms. This is useful if you are interested in specific residues involved in processes, like protein-ligand interactions.

gmx mindist calculates the minimum distance and number of contacts between pairs of atoms.

Note

You will need to use a custom index file if you are measuring distance between custom groups of atoms.

You should have the following files for both commands:

  • Trajectory files (.xtc)
  • Topology file (.tpr)
  • Index file (.ndx)

Using gmx distance

To calculate distances between fixed pairs:

gmx distance -f trajectory.xtc -s topology.tpr -n index.ndx -tu ns -select 'first group' 'second group' '...' -oav avg-dist.xvg -oxyz comp-dist.xvg

-select allows you to directly indicate which groups you want to analyze, which is convenient for slurm scripts. If the -select option is not used, you will be presented with a group selection menu after running the command.

Group selection menu in gmx distance.

Note that gmx distance can take more complex selections than what is typical of standard index files. Enter help examples in the prompt for examples.

This produces the following outputs:

  • -oav: average distances as a function of time
  • -oxyz: distance components (x-/y-/z-axis) as a function of time
  • These XVG files can be visualized using Python or Grace to produce a plots of distance versus time, or to generate a heat-map.

Using gmx mindist

To calculate the minimum distance between pairs:

gmx mindist -f trajectory.xtc -s topology.tpr -n index.ndx -d <nr> -tu ns -od mindist.xvg -on count.xvg -or mindist-res.xvg -group

-group tells GROMACS that all contacts between one atom in a group and multiple atoms of the other group should be considered a single contact. -d specifies the distance cut-off in angstroms for a pair to be considered in contact.

You will then be prompted to select two groups to measure distances between.

This produces the following outputs:

  • -od: minimum distances between pairs of atoms
  • -on: number of contacts between pairs of atoms
  • -or: minimum distances to residues in group 1, plotted as a function of residue number

Additional Resources