AMBER Archive (2005)

Subject: AMBER: Moil view trajectory clusters

From: Austin B. Yongye (ayongye_at_sunchem.chem.uga.edu)
Date: Thu Feb 17 2005 - 11:36:15 CST

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?
Thanks,
Austin-

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