Hi, tahnks for the reply.

At the moment I have calculated the distance between molecules and the angle. This information is stored in 992*2 files. The reason is more related to the way I calculated the data, but I could easily store this in a matrix in a single file too. However my challenge is to translate the analysed data 1_3 1_5 5_7 9_23 14_23 17_20 into number of clusters and cluster sizes at each timestep. I dont care if this is stored in a single file, but it is the two parameters that informs me if a simulations is successful.

yep, clusters may be formed and dissolved over time.

Hope this helps abit I know it is difficult when I have no initial code :)