[gmx-users] Generating Structures from Covariance Matrix Eigenvectors

[Tsjerk Wassenaar]

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 <spoel at xray.bmc.uu.se> 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   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