Water molecules clustering algorithm

Algorithm was designed to cluster water particles from MD simulations based on their coordinates into equally sized groups.

Algorithm was designed to cluster water particles from MD simulations based on their coordinates into equally sized groups. It is used to aggregate non-bounded MD (water) molecules in order to map their parameters into the coarse-grained model (such as based on dissipative particle dynamics). See the publication below for a full description of the procedure:

Pieczywek, P.M., Płaziński, W. & Zdunek, A. Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations. Sci Rep 10, 14691 (2020). https://doi.org/10.1038/s41598-020-71820-2

The input data should be a matrix containing the coordinates of the molecules for the successive MD simulation frames. Sample data is included in the file "test_data.mat". Script “example.mat” clarifies how the functions works.