Convex Hull Volume and Density [1]

../_images/12ConvHull.png

The convex hull of a particle is the smallest convex shape that can enclose all atoms of the particle. In MakroLyzer, the convex hull is computed using scipy.spatial.ConvexHull [2]. The volume of the convex hull can be used as a measure of the particle’s desnity, which is calculated as the mass of the particle divided by the volume of the convex hull.

Because the convex hull approximates the spatial extent of a particle, it can be used to determine whether other particles penetrate the selected particle. For example, in a solvated polymer, this makes it possible to count how many solvent molecules have their center of mass within the polymer’s convex hull.

Command line

-ConvHullVol
--convexHullVolume
Calculate the volume of the convex hull spanned by a particle. Additionally, the mass of the polymer as well as the density (mass/volume) are calculated. Optionally provide an output filename
Default: ConvexHullVolume.csv

-ConvHullSol PARTICLE_SEL SOLVENT_SEL
--convexHullSolvent PARTICLE_SEL SOLVENT_SEL
Calculate the convex hull of the selected particle molecules and count how many selected solvent molecules have their center of mass inside that hull.
The two selections use the same subgraph-selection syntax as --hb-between.
Default output: ConvexHullSolvent.csv

-ConvHullSol-file
--convexHullSolvent-file
Optional output filename for the convex-hull solvent count.

Example

MakroLyzer -xyz polymer.xyz -ConvHullVol
MakroLyzer -xyz solvated_polymer.xyz -ConvHullSol CHON H2O

Output

Each row starts with the frame index followed by the volume of the convex hull, the mass of the particle and the density (mass/volume) in CSV format. For solvent counting, each row starts with the frame index followed by the particle selection, solvent selection, convex hull volume and the number of solvent molecules inside the convex hull.