AMBER Archive (2009)

Subject: Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors

From: Hannes Loeffler (
Date: Fri Feb 13 2009 - 02:32:20 CST

You can compute the first N projections with the "beg" and "end"
parameters of the "projection" command which gives you N 1D trajectories
along the corresponding eigenvectors. In the output file you should see
several columns each containing one 1D trajectory. The second line
tells you which is which. Plot the two columns that you want against
each other as you like.

I do not understand your last sentence. A projection is a dot product
between two vectors naturally yielding a scalar. I do not see how you
could possibly obtain vectors in this way.

On Thu, 2009-02-12 at 12:22 -0600, Carra, Claudio (JSC-SK)[USRA] wrote:
> Dear All,
> is there a way in amber to calculate the projections
> of trajectories onto the first 2 principal eigenvectors?
> I'm interested in looking at the distribution densities.
> I would expect a matrix but if I use "projection"
> I get 2 vectors.

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