[gmx-users] regarding the cosine content analysis

[Ahmet yıldırım]

Dear users,

I performed MD simulation of 400 ns of a structure. I used the cosine
content to check whether the simulation is not converged. I used last 100
and 50 ns of trajectory to the analysis, respectively. The results were
very similar to each other.The cosine contents of the first ten principal
components are as follows. The cosine contents of the principal components
are very small but one. Why is the second cosine content differs from the
others? What could be the reason for this? And do you think simulation has
reached convergence?

The cosine contents of last 50 ns:
 1 0.00685769
 2 0.137028
 3 0.00139929
 4 0.00903137
 5 0.0180072
 6 0.0128686
 7 0.00154502
 8 9.71793e-05
 9 0.00485945
 10 0.00202377

Thanks in advance
-- 
Ahmet Yıldırım