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?