GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear all,
We are doing the cluster analysis by gmx cluster command and there are formation of cluster.log and cluster.pdb file with number of cluster founds 6 with RMSD cutoff 0.7 nm, and we found that number of cluster are decreasing with decrease in cutoff from 1.2 nm to 0.7 nm by 1. I am little bit confusing about the selection of cutoff and anybody give me the idea about writing the percentage of each cluster.
Please suggest me regarding this
Hi
about writing the percentage of each cluster
you can look at the ratio of number of structures in one cluster on to the total number of structure in the trajectory. That provides the % of structures in your sampling
Best regards
Alessandra
thank you for the reply