Hi Robert,
The g_anaeig option -extr is for the extreme projections onto a (set
of) eigenvector(s). You want to use the option -filt, which does
precisely what you request, returning you a filtered trajectory. I.e.
the "noise", the fluctuations on non-selected eigenvectors, is
filtered out.
Cheers,
Tsjerk
On 2/1/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Robert Johnson wrote:
> Hello everyone,
> I'm new to Principle Components Analysis, so correct me if I'm wrong.
> If you have a collection of protein structures from a replica exchange
> calculation, for example, I believe you can reconstruct each of them
> from its average structure by the following:
>
> r(t) = <r> + p_1(t) v_1 + p2(t) v_2 + p_3(t) v_3 + ... + p_N(t) v_N
>
> Here, r(t) is the protein configuration at time t, <r> is the average
> structure, p_i(t) are the projections of the structure at time t on
> the i-th eigenvector and v_i is the i-th eigenvector of the covariance
> matrix. Of course, to capture the large scale motion, one would be
> interested in only the first or second projections. For example, it
> would be of interest to compute
>
> r(t) = <r> + x v_1
>
> Here, the value of x could be varied to observe the motion of the
> protein along v_1.
>
> I'm wondering if there is a feature in g_anaeig (or another program)
> that does this? I didn't find this option, but thought I would ask to
> make sure.
> Thanks,
> Bob
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g_anaeig -extr
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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