[gmx-users] regarding the cosine content analysis

[Thomas Evangelidis]

You don't do it the right way. You must start the analysis from the
beginning not from the end of your trajectory. I.e.

0-20ns
0-30ns
0-40ns
...
0-100ns

Until the cosine content of the first 3 principal components that account
for most of the variance in the atomic fluctuation have been dropped at
least once below 0.5. This is the point where theoretically the system has
equilibrated enough.

Thomas


On 22 February 2013 13:43, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:

> 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
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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/