[gmx-users] Projecting conformational changes onto PCs

[Tsjerk Wassenaar]

Hi Raul,

The answer to a question with 'projection' and 'eigenvector' is g_anaeig.
But you project a structure, not a difference vector. You can also
calculate the inner product between two sets of eigenvectors, or between a
delta vector and a set of eigenvectors, again using g_anaeig (-inpr). I
think that is what you want here.

Cheers,

Tsjerk
On Apr 1, 2014 11:24 PM, "rmendez" <rmendez at email.unc.edu> wrote:

> Hi Tsjerk,
>
> Thanks for your answer, but g_anaeig (among other things) gives the
> projection of each snaphot of my trajectory onto the selected PCs along
> time. What I want is the projection of a different structure, for instance
> the difference between my protein into a closed conformation (different
> from
> the open conformation that I used in the MD simulations). Ideally I would
> have a Delta_R vector (3N vector) after superposing conformation 2 onto 1.
> This is the vector I would like to project onto the first N PCs, so the
> projections would tell me how much each PCs contribute to the observed
> conformational change. I guess there is no tool to do that on gromacs
> (although there are all the ingredients needed), is there ?
>
> Thanks,
>
> Raul
>
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