Hi all, I have a couple of questions regarding g_covar: First, is there anyway to specify that the covar.dat output will be in R distance (meaning sqrt(x^2+y^2+Z^2)) and not in separate Cartesian coordinates? also when examining the output I don't understand how the main diagonal values are different than 1, for instance the x1x1 covariance should be 1.. or am I missing something?
Second, Say I would like to analyze the main difference between two trajectories of the same protein using PCA. is it KOSHER to use the same first frame which is identical between both runs as the reference strucutre and then just append both runs into a single trajectory and then use g_covar to analyse the subsequent conformations? if not, how would one go about comparing the PC's of two different trajectories? other than dumping all the frames in gro/pdb format and running the analysis in another program (such as MATLAB) Thanks, Gideon
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