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

From: Carlos Simmerling via AMBER <>
Date: Fri, 9 Sep 2022 10:56:52 -0400

it's an option in cpptraj, you might want to look at

On Fri, Sep 9, 2022 at 10:49 AM ning via AMBER <> wrote:

> 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 - 08:00:03 PDT
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