[gmx-users] g_covar

גדעון לפידות glapidoth at gmail.com
Tue Aug 16 09:18:01 CEST 2011

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


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