[gmx-users] PCoorA and Energies

andrea spitaleri spitaleri.andrea at hsr.it
Tue Mar 20 13:45:08 CET 2007

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



Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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