Hi Tsjerk,
I computed r.m.s.i.p. between eigvectors trajectory for two halves of
the same simulation, I expected it should be higher value than its other
eigenvectors. But in my case it is showing less than the others, For
example, please look at the below r.m.s.i.p matrix
Wild Mutant1 Mutant2 Mutant3
Wild 0.630693 0.650160 0.65414 0.632176
Mutant1 - - - -
Mutant2 - - - -
Mutant3 - - - -
Other values of the matrix not computed yet, but please comment on this
output, Is it possible? For Wild Vs Wild of 2ns simulation run, I
generated eigenvector trr file using g_covar program for first 0 to 1ps
and it was repeated for 1ps to 2ps. and finally I used both trajectories
to compute r.m.s.i.p. value.
With thanks!
B.Nataraj
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