[gmx-users] CLUSTERING:Number of clusters as function of time.

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 31 09:15:01 CET 2003

On Fri, 31 Oct 2003, Mr.Sridhar wrote:

>I wanted to know the number of conformations the protein has taken in my
>MD run trajectory. For this I am clustering the snapshots using g_cluster.
>I mainly wanted to know how the number of clusters varies with time.
>In the result file (clust-id.xvg), I found the number of clusters increase
>and decrease. To my knowledge, the number of clusters should steadily
>increase with time and then reach a plateau where the system visits no
>more new conformations.
You can have at most one cluster per timestep. I think clust-id.xvg gives
you something else. In fact I think it first does the cluster analysis
over the complete trajectory, and then this file goves you for each
timestep the cluster-identification number.

>Could any body explain why the number of clusters
>show fluctuations of high and low values instead of gradually increasing
>with time?
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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