AMBER: Moil view trajectory clusters

From: Austin B. Yongye <>
Date: Thu, 17 Feb 2005 12:36:15 -0500 (EST)

Amber users,
I am using moil view to cluster an MD trajectory and also perform 2drmsd
analyses. First I did the 2drmsd, with rmsd cutoff criteria: Low 0-1,
middle 1-2, high 2-3. This gave me 2 conformer families. However, when I
cluster the trajectory, using an rmsd cutoff of 1Ang, 7 clusters are
produced. Why do I get this difference?
Also, regardless of the number of frames in the trajectory, the clustering
always gives only 400 frames. Any possibility of getting more frames?

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Received on Thu Feb 17 2005 - 17:53:00 PST
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