Dear researcher
I am facing a problem in principle component analysis. I calculated the eigenvalue by g_covar command. After that i saw in many Literaturrates they give the percent value.
In articles they describe such type
“The first few eigenvalues are relative to concerted motions, and quickly decreased in amplitude to reach a number of constrained, more localized fluctuations. This analysis suggests that the first 20 principal components (PC) can account for 58.8%, 56.0% and 60.2% of the motions observed in the last 30 ns of the trajectories for WT, D181A and D181E,respectively”
Note- These lines was taken from article. I also attach articles
How they calculated percent of motions by .xvg file. I also attach figure
Dear james sir
I calculated the % of eigenvalues. Then i want to calculate eigrmsf. When i give the command it gives the motion ATOM wise. How can i convert this plot in to residue.
Please suggest me some tutorial about principle component analysis also
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