Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ?
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