Re: [AMBER] pseudo F-statistic (pSF)

From: Jonathan Gough <>
Date: Thu, 8 Jan 2015 12:20:33 -0500

Thanks Gentleman, Very helpful! (I found the rms2d command and am playing
with it now)

On Thu, Jan 8, 2015 at 12:05 PM, Thomas Cheatham <> wrote:

> add to what Dan said, ptraj development was effectively ended prior
> to the wide-spread adoption of netCDF files; think of the ptraj clustering
> code as "tests" for various clustering algorithms.
> In an ideal world, where the data is clearly disjoint, the clustering
> algorithm does not matter. In the case where transitions between clusters
> is smooth, and the breaking point from one cluster to another is somewhat
> arbitrary (depending on your choice of metric, statistics, definition of
> centroid or "membership" in a cluster), the results do depend on the
> clustering and there is no one "right" way to do this. This is the case
> with MD data usually. What we do is explore choices of clustering that
> provide the information we are trying to decipher. An excellent example
> is the Henriksen et al. paper from 2013 on the GACC tetranucleotide, where
> Niel went through many test/iterations to find a way to partition the data
> in a meaningful way.
> What I often do to figure out how many clusters is to do a 2D RMSD plot
> since this is easy to see visually.
> CPPTRAJ does not re-implement all the algorithms for clustering of ptraj
> since we didn't think it necessary...
> Hope this helps, --tec3
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Received on Thu Jan 08 2015 - 09:30:04 PST
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