4.3.4. Simple atomic distance analysis — MDAnalysis.analysis.atomicdistances

Author:

Xu Hong Chen

Year:

2023

Copyright:

GNU Public License v3

This module provides a class to efficiently compute distances between two groups of atoms with an equal number of atoms over a trajectory. Specifically, for two atom groups ag1 and ag2, it will return the distances

\[|ag1[i] - ag2[i]|\]

for all \(i\) from \(0\) to n_atoms \(- 1\), where n_atoms is the number of atoms in each atom group. By default, this computation is done with periodic boundary conditions, but this can be easily turned off. These distances are grouped by time step in a NumPy array.

For more general functions on computing distances between atoms or groups of atoms, please see MDAnalysis.analysis.distances.

See also

MDAnalysis.analysis.distances, MDAnalysis.lib.distances

4.3.4.1. Basic usage

This example uses files from the MDAnalysis test suite (GRO and XTC). To get started, execute

>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import GRO, XTC
>>> import MDAnalysis.analysis.atomicdistances as ad

We will calculate the distances between an atom group of atoms 101-105 and an atom group of atoms 4001-4005 with periodic boundary conditions. To select these atoms:

>>> u = mda.Universe(GRO, XTC)
>>> ag1 = u.atoms[100:105]
>>> ag2 = u.atoms[4000:4005]

We can run the calculations using any variable of choice such as my_dists and access our results using my_dists.results:

>>> my_dists = ad.AtomicDistances(ag1, ag2).run()
>>> my_dists.results
array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
       [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
       [23.27210749, 30.38714688, 32.48269361, 31.91444505, 31.84583838],
       [18.40607922, 39.21993135, 39.33468192, 41.0133789 , 39.46885946],
       [26.26006981, 37.9966713 , 39.14991106, 38.13423586, 38.95451427],
       [26.83845081, 34.66255735, 35.59335027, 34.8926705 , 34.27175056],
       [37.51994763, 38.12161091, 37.56481743, 36.8488121 , 35.75278065],
       [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
       [38.76272761, 41.31816555, 38.81588421, 39.82491432, 38.890219  ],
       [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

To do the computation without periodic boundary conditions, we can enter the keyword argument pbc=False after ag2. The result is different in this case:

>>> my_dists_nopbc = ad.AtomicDistances(ag1, ag2, pbc=False).run()
>>> my_dists_nopbc.results
array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
       [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
       [23.27210749, 30.38714688, 32.482695  , 31.91444505, 31.84583838],
       [18.40607922, 39.21992825, 39.33468192, 41.0133757 , 39.46885946],
       [26.26006981, 37.99666906, 39.14990985, 38.13423708, 38.95451311],
       [26.83845081, 34.66255625, 35.59335027, 34.8926705 , 34.27174827],
       [51.86981409, 48.10347964, 48.39570072, 49.14423513, 50.44804292],
       [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
       [56.39657447, 41.31816555, 38.81588421, 39.82491432, 38.890219  ],
       [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

class MDAnalysis.analysis.atomicdistances.AtomicDistances(ag1, ag2, pbc=True, **kwargs)

Class to calculate atomic distances between two AtomGroups over a trajectory.

Parameters:

• ag1 (AtomGroup) – AtomGroup with the same number of atoms

• ag2 (AtomGroup) – AtomGroup with the same number of atoms

• pbc (bool, optional) – If True, calculates atomic distances with periodic boundary conditions (PBCs). Setting pbc to False, calculates atomic distances without considering PBCs. Defaults to True.

results

The distances \(|ag1[i] - ag2[i]|\) for all \(i\) from \(0\) to n_atoms \(- 1\) for each frame over the trajectory.

Type:

numpy.ndarray

n_frames

Number of frames included in the analysis.

Type:

int

n_atoms

Number of atoms in each atom group.

Type:

int

Added in version 2.5.0.