Well, the cosine content doesn't tell you very much anyway. And
fitting a cosine with a full period to the second component only makes
sense if the first fits well to a half cosine. If the correlation
coefficient is about .1, it tells you less. It says nothing,
absolutely nothing about convergence
Then, these cosine content's results are all normal?
2013/2/25 Tsjerk Wassenaar
> Because it fits a little bit better to a cosine with full period than
> the first one fits a cosine with half period and the third one fits a
> cosine with 1.5 period.
>
> Tsjerk
>
> On Mon, Feb 25, 2013 at 1:23 PM
Because it fits a little bit better to a cosine with full period than
the first one fits a cosine with half period and the third one fits a
cosine with 1.5 period.
Tsjerk
On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım wrote:
> Hi,
>
> I think my question was misunderstood.
> My question is:
> W
Hi Thomas,
Okay :) First of all, do be careful that the first stage of
relaxation, giving that nice principal component profile, is not
exclusive. If you take it off, by leaving out the first part of the
trajectory, you may well find that there is another component which is
still relaxing, which m
Hi,
I think my question was misunderstood.
My question is:
Why is second cosine content greater than the other values?
Regards
2013/2/25 Thomas Evangelidis
> On 25 February 2013 12:14, Tsjerk Wassenaar wrote:
>
> > Hi Thomas,
> >
> > As I've explained previously, the cosine content does not a
On 25 February 2013 12:14, Tsjerk Wassenaar wrote:
> Hi Thomas,
>
> As I've explained previously, the cosine content does not allow such
> inferences. Besides, taking the relaxation from the start into account
> in PCA is pretty nonsensical, unless you aim to characterize that
> relaxation in the
Hi Thomas,
As I've explained previously, the cosine content does not allow such
inferences. Besides, taking the relaxation from the start into account
in PCA is pretty nonsensical, unless you aim to characterize that
relaxation in the first place. Looking at the cosine content to infer
equilibrati
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 a
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 princi
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