Re: AMBER: Moil view trajectory clusters

From: Austin B. Yongye <>
Date: Thu, 17 Feb 2005 16:31:37 -0500 (EST)


> 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?
>>The AMBER Mail Reflector
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Received on Thu Feb 17 2005 - 21:53:01 PST
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