How to obtain water cluster index file?

User discussions
1

Dear all,

I want to analyze water cluster in my (polymer/water) system. Average number of clusters is 4. I want to know if it is possible to obtain index file for each cluster at a specific time? I want to distinguish them in vmd and I need index file of each water cluster.Gromacs just gave me maxclust.ndx.(maximum cluster size index)

Thank you in advance

2

Hi,
a tools to generate dynamics index is gmx select.
Here you find something on selection synthax
https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection
maybe it helps
Best regards
Alessandra