[gmx-users] Reference structure for g_covar

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 19 13:58:00 CEST 2011

Hi Vivek,

I explained related matters in some detail on this list earlier, and
would urge not to use a structure other than the average for
determining the components.

The results on the cosine contents can be illustrated as follows:

I. Using average

Imagine you're moving from place A to place B. The principal component
is B-A, and the average is (A+B)/2. Your score/projection is the
position relative to the average; negative on one side, positive on
the other. This ends up being a straight line in one dimension, but in
higher dimensions you'll get a nice half cosine.

II. Using fixed reference

Let's say your reference is A, then your component is still B-A, but
your score/projection is now the distance from A. It starts out at
zero and increases. In higher dimensional space, this would give a
projection that starts out approximately linear and levels off at some
point. These components are awkward, and very hard to interpret.

Hope it helps,


On Wed, Oct 19, 2011 at 10:08 AM, vivek modi <modi.vivek2009 at gmail.com> wrote:
> Hi,
> I am doing Essential Dynamics on a protein (150 residues). The simulation is
> 100ns long and the RMSD becomes very stable after 25ns.
> I have gone through the mailing list archives but could not find a precise
> answer to the following question.
> When I calculate the cosine content for the first PC by taking the average
> structure for fitting using g_covar it gives a very high value ~.8.
> But when I change the reference structure to the starting structure then I
> get a cosine value ~.1.
> I also repeated the same by dividing my trajectory into two equal halves but
> the cosine value with average structure as a reference is always very high
> while it is reasonably low with starting structure taken as reference.
> My question is why the cosine content is dependent on the fitting
> structure used in g_covar?  And, especially, which structure is
> recommended to use in Essential Dynamics analysis ?
> Any help is appreciated.
> Thanks a lot.
> Regards,
> Vivek Modi
> Graduate Student,
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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