[gmx-users] eigenrmsf in COMBINED ESSENTIAL DYNAMICS

[Tsjerk Wassenaar]

Hi Sridhar,

Using this procedure, the frames from either trajectory will project
to either side of the mean (0) on each eigenvector, and are therefore
expected to be the same on average, except for the sign, which you
loose by taking the variance. You should calculate the variance for
the trajectories on each eigenvector using the mean projection of that
trajectory in order to compare the two.

Cheers,

Tsjerk

On 2/6/07, sridhar at cdfd.org.in <sridhar at cdfd.org.in> wrote:
> I am getting the following unexpected results, from a COmbined Essential
> dynamics analysis.
> I have concatenated two trajectories of MD runs of similar systems.
> Then I ran g_covar to get the eigenvectors and eigenvalues.
> Then I ran g_anaeig to find the projections and rmsf fluctuations of the
> separate individual trajectories when projected onto the combined eigen
> vectors.
> As expected the projections of each individual trajectories were different
> on the combined eigen vectors. But I get the eigen_rmsf plots exactly the
> same for both the trajectories. I tried this for several times but could
> not locate the fault in the command submission. Can anybody throw light on
> what could be going wrong?
>
> Thanking you,
>
> sridhar acharya.
>
>
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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