Surface Atoms [1]

This analyzer identifies surface atoms of a polymer particle and classifies them into:

  • nonpolar surface atoms

  • polar surface atoms

  • ring surface atoms

Surface atoms are detected with the GITIM method [2] as implemented in pytim [3] on an MDAnalysis universe [4]. Ring surface atoms are carbon atoms that belong to cycles matching the selected ring-size criterion.

Command line

-sA
--surfaceAtoms
Identify and count nonpolar, polar, and ring atoms on the particle surface.
Optionally provide an output filename.
Default: surfaceAtoms.csv

--sA-ring-size
Ring-size filter used for ring atom assignment.
Accepts a single ring size (e.g. 6) or an inclusive range (e.g. [4,7]).
Minimum allowed ring size is 3.
Default: 6

Example

MakroLyzer -xyz polymer.xyz -sA surfaceAtoms.csv --sA-ring-size [4,7]

Output

The output file contains one row per frame:

Column

Description

Frame

Frame index in the trajectory

Nonpolar Surface Atoms

Number of surface atoms classified as nonpolar

Polar Surface Atoms

Number of surface atoms classified as polar

Ring Surface Atoms

Number of surface carbon atoms that belong to rings matching --sA-ring-size