[gmx-users] Principal Component Analysis (PCA)

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Nov 25 20:57:45 CET 2012


The eigenvectors are dependent on the orientation of the conformations,
which you fix prior to PCA by fitting the structures to a reference. If you
want to project another simulation onto a set of eigenvectors you already
have, you have to fit it to the same reference structure, using the same
procedure (e.g. mass-weighted or not).

Hope it helps,


On Sun, Nov 25, 2012 at 9:38 AM, harshaljain950 <harshaljain950 at gmail.com>wrote:

> hi all,
> Can we plot RMSF versus atom numbers using eigenvectors of a different
> simulation and trajectory of another simulation.
> I know we can plot RMSF versus atom numbers using the eigenvectors and
> trajectory of a same simulation using g_anaeig
> Thanks in advance
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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