[AMBER] How to determine the optimal number of cluster in cpptraj or other something

From: ning via AMBER <amber.ambermd.org>
Date: Fri, 9 Sep 2022 22:48:34 +0800 (CST)

Hi Amber experts,
      I need to do a clustering analysis for a long time molecular dynamic simulation, about 2 microsecond. I had finished the cpptraj tutorial for clustering. The dbscan method may occupy too much memory storage and computation time. I choose the k-means method, whereas, I don't know how to determine the best number of clusters in trajectory processing. I read some papers that mentioned a method called "silhouette" which is able to calculate the differences between one cluster and one's neighboring cluster. I want to know how to acheive this function in CPPTRAJ tool. Any suggestions are welcome, please help me. Thanks in advance.

AMBER mailing list
Received on Fri Sep 09 2022 - 08:00:02 PDT
Custom Search