AMBER Archive (2005)

Subject: Re: AMBER: Moil view trajectory clusters

From: Austin B. Yongye (ayongye_at_sunchem.chem.uga.edu)
Date: Thu Feb 17 2005 - 15:31:37 CST

Thanks!!!!

> 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: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
>
>
> 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?
>>Thanks,
>>Austin-
>>
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Dr. Woods' Research Group
University of Georgia
Complex Carbohydrate Research Centre
315 Riverbend Road
Athens, GA 30602

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