Hi,
As prof. Simmerling pointed go to the cluster analysis command in pp 786 of amber manul 22. You can see a option "sil". Use that command to calculate cluster silhouette value.
Best,
Satyajit Khatua
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________________________________
From: ning via AMBER <amber.ambermd.org>
Sent: Friday, September 9, 2022 8:18:34 PM
To: amber maillist <amber.ambermd.org>
Subject: [AMBER] How to determine the optimal number of cluster in cpptraj or other something
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.
Sincerely,
Ning
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Received on Fri Sep 09 2022 - 08:30:02 PDT
