Re: AMBER: Moil view trajectory clusters

From: Carlos Simmerling <>
Date: Thu, 17 Feb 2005 13:19:50 -0500

the the 2d-rmsd with smooth shading, sometimes imposing specific ranges
can cause artifacts. then use the smooth shading to help choose a cutoff
for the clustering.

for more frames, you need to change the limits in LENGTH.BLOCK.
It still calculates the entire 2D matrix, which can be very slow. You might
want to use ptraj, which can cluster with a 2-pass approach using sieving
on the first pass. This is much faster for very large data sets.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Austin B. Yongye wrote:

>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 - 18:53:00 PST
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