[gmx-users] Regarding cosine content

[bipin singh]

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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Regards,
Bipin Singh