clustering analysis

[lauraf244]

Hello,

can anyone help me with the right code to perform a clustering analysis on a .xtc file from a LAMMPS simulation?
And which is the right approach to perform the clustering? i.e. selecting atom positions? Distances?
If my system is a liquid phase caracterized by hydrogen bonds, should i select for example the H--O distance for 1 couple of molecules or for all the molecules of the systems to perform the clustering? How to do it?

Thank yoi very much for the help!

[orbeckst]

This seems to be more of a science question: Read the literature on systems like yours to find out what the usual way is to analyze them. Once you have a specific idea what you want to do, you can look into the how to use MDAnalysis to make your idea a reality.

There are various MDAKits related to liquid analysis and clustering such as solvation-analysis, maicos, MDANCE, mdaencore (the latter two for proteins as far as I know).