self-assembly treatment

Hi all,

I ran a md simulation of a CG model of my peptide. The aim of the simulation is to study whether the peptide will self-assemble in ordered structures or not. Once I’ve run the symulation, it is difficult to actuall see whether there is any order in the aggregates, so I wanted to perform a radial distribution funciton study. In order to to that I would like to isolate only one aggregate. I tried using gmx_cluster and the clustering method to be ex. Jarvis-Patrcik. But the problem is that I couldn’t get an index file for each of the cluster found (-clndx was not recognized as a funciton).
Does anyone has any advice on how to perform such analysis?


gmx cluster is a tools to cluster structures using seveal different methods, not to idenfity aggregate between structure. To identify aggregates, maybe some like gmx clustsize is more appropriate

Best regards

Hi Alessandra,

Thank you very much for the advice! It really helped