Hi Tsjerk,
Thank you for all the clarifications. Just one more thing, I excluded the
loop residues with RMSF>4 A. (because their movement is dominated by random
diffusion), did PCA on the rest of the protein, and the cosine content
improved significantly. Is this procedure acceptable?
Thanks in a
Hi Thomas,
First of all, proteins in solution don't suddenly stop with Brownian
motion at some point. It's just the way things move at the microscopic
level. Second, the cosine content has nothing to do with randomness.
Really. Nothing. On the contrary. The cosine content indicates
unidirectional
Dear Tserk and the rest of GROMACS users,
Last time I measured the cosine content of different time intervals from
the PCs of the whole trajectory. This time I did PCA for each time interval
and measured the cc which is the right way I suppose. Maisuradze et al.,
2009 claim that a CC value below 0
Hi Thomas,
Whether or not it makes sense to do PCA on the domain only depends on
the question you ask. It may well make sense if you aim at
characterizing the intra-domain motions. But be aware that you will
view those motions within the context of the rest of the protein. It
is quite likely that
Regarding my second question, I have been experimenting with the cosine
content using different portions of the trajectory and these are the
results I got for the first principal component:
proj-ev1_coscont_0-5ns.xvg 0.0174761
proj-ev1_coscont_0-10ns.xvg 0.0283423
proj-ev1_coscont_0-15ns.xvg 4.169
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