[gmx-users] Help with Principal component analysis

Alex Jemulin alexbioinfo at yahoo.com
Mon Jan 2 20:54:04 CET 2012

Dear all
I run a MD on a GPCR (transmembrane protein)
Then I run a PCA on results and I found 3PC sufficient to explain variance.
On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and Loop5 (intracellular).According to you how could I explain the motion of group atoms intra and extracellular on the same components? 
Does it mean the motion of some atoms at Nter (for instance) could influence the motion at Cter ? Could it be logic?
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