What conclusions can we made from principal component analysis?

User discussions
1

GROMACS version: 2018.1
GROMACS modification: Yes/No

  1. If a protein has a high trace value and covers a large area in the conformational space then can we say that protein has an impairment in its activity? And if so, how can we justify the point?
  2. The commands gmx covar and gmx anaeig gives the projection of the protein motion along first two principal components. But, in an article I have seen a plot of PC1 versus simulated time. Does anyone know how to get a plot PC1 with respect to time?