[gmx-users] PCoorA and Energies

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 20 14:27:30 CET 2007

Hi Andrea,

You have a different energy landscape for each temperature. For a
given point in conformational space, the energy of your system will be
higher with higher temperatures. However, the energies will not only
be shifted, but the shift will depend on the position in
conformational space (so wells will become shallower and barriers will
be crossed more easily). In short, no, you can't just plot the
energies over the "principal coordinates" and construct an energy
landscape, you'll have to do it for the different temperatures
seperately (which would be nice for an illustration though). Note that
distance in PCoorA will be "conformational distance", i.e. the RMSD.



On 3/20/07, andrea spitaleri <spitaleri.andrea at hsr.it> wrote:
> Hi guys,
> principal coordinate analysis (PCoorA) is a variant of the classical PCA. It is the covariance
> matrix of the distances. Becker et al. (JCP 1998,19,1255 and 2001,114,993) sentences that the PCoorA
> reflects the relationship between the conformations rather than the coordinates as in the classical
> PCA study. In his study he reported that plotting PCoorA-1 and/or PCoorA-2 (1st and 2nd principal
> coordinate axis) versus the Energies one can extract a potential energy surface in order to study
> the different weight of the various conformers.
> Now, I have performed a REMD (2ns x 15 replicas) of my small peptide and I did the usual analysis on
> the 30ns trr trajectory.
> I am wondering now whether plotting the PCoorA-1/2 versus the Energies from the REMD makes
> physically sense, since the total energy.edr is coming from different temperatures.
> Any hints? any suggestions?
> Thanks in advance
> Regards,
> andrea
> --
> -------------------------------
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> http://biomolecularnmr.ihsr.dom/
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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

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