What it does

This tool calculates and plots the distance between pairs of atoms. Two modes are available: single pair mode, where distances are calculated between two specified atoms, and multiple pair mode, where two lists of atoms need to be provided.

Input

• Trajectory file (DCD).
• PDB file.

In single pair mode, segment IDs, residue IDs and names of two atoms are selected. Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

In multiple pair mode, two files need to be uploaded, each with one or more atom groups defined using the MDAnalysis atom selection, each on a new line. For example:

resid 163
resid 56
resid 12 and type N

All possible distances between the two sets of atom groups will be calculated. For example, if List 1 contains 5 atoms and List 2 contains 8 atoms, the output file will contain 40 columns, each with the distance between one group in List 1 and one group in List 2.

Note that in multiple pair mode, if the group has multiple atoms, the center of mass will be used for the calculation.

Output

• Tab-separated file of raw data of distance between two atoms calculated for each frame.
• Image (as png) of the time series graph.