Hydrogen Bonds [1]

This analyzer counts hydrogen bonds using geometric cutoffs.

Additionally, the hydrogen bond count can be calculated between two selections, like between a polymer and the solvent.

Command line

-hb A:b:c:alpha

--hydrogenBonds

Count hydrogen bonds for one or more acceptor types.
A is the acceptor element symbol
b is the maximum hydrogen atom (H) - acceptor atom (A) distance (float)
c maximum donor atom (D) - acceptor atom distance (float)
alpha is the maximum angle in degrees between the D-H and H-A vectors (float)

-hb-file

--hbonds-file

Output filename.
Default: hydrogenBonds.csv

-hb-pos

--hbondPositions

Write one XYZ file per frame with H-bond midpoint positions.
Requires --hydrogenBonds.
Optionally provide a base output filename.
Default: hbondPositions.xyz

-hb-between SEL1 SEL2

--hb-between SEL1 SEL2

Count only hydrogen bonds between two selected species.
Requires --hydrogenBonds to define the hydrogen-bond cutoffs.
Hydrogen bonds within either selected species are ignored.
The selections use the same subgraph-selection syntax as -sel.

-hb-between-file

--hb-between-file

Output filename for hydrogen bonds between two selections.

Default: hydrogenBondsBetween.csv

Example

MakroLyzer -xyz polymer.xyz -hb O:2.4:3.4:30 -hb-file myHbondOutput.csv
MakroLyzer -xyz solvated_polymer.xyz -hb O:2.4:3.4:30 -hb-between CHON H2O
MakroLyzer -xyz polymer.xyz -hb O:2.4:3.4:30 -hb-pos myHbondPositions.xyz

Output

The output file contains one row per frame and cutoff:

Column	Description
Frame	Frame index in the trajectory
Element Type	Acceptor element symbol
H-Acceptor dist	Cutoff distance `b`
Donor-Acceptor dist	Cutoff distance `c`
Angle cutoff	Cutoff angle `alpha` (degrees)
Number of Hydrogen Bonds	Count for this cutoff

For hydrogen bonds between two selections, the output file contains the same cutoff information and additionally lists the two selections:

Column	Description
Frame	Frame index in the trajectory
Selection 1	First selected species
Selection 2	Second selected species
Element Type	Acceptor element symbol
H-Acceptor dist	Cutoff distance `b`
Donor-Acceptor dist	Cutoff distance `c`
Angle cutoff	Cutoff angle `alpha` (degrees)
Number of Hydrogen Bonds	Count of hydrogen bonds between the two selections for this cutoff