[gmx-users] Re: regarding the cosine content analysis

[Ahmet yıldırım]

Dear users,

I did not get any response in my last email. Any help will be appreciated.

Thanks in advance
2013/2/22 Ahmet yıldırım <ahmedo047 at gmail.com>

> 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
>



-- 
Ahmet Yıldırım