[gmx-users] regarding the cosine content analysis
tsjerkw at gmail.com
Mon Feb 25 11:14:53 CET 2013
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
equilibration from that is blatantly fooling yourself.
If you feel you must use cosine content to support any claim on
equilibration, then it is a much better approach to start from the end
of the simulation and check that the stretch of the trajectory you
take does not yield high cosine contents, in which case you have some
reason to argue that that part of the simulation is sampled in a local
On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> 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.
> 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.
> 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
> 157 71 Athens
> email: tevang at pharm.uoa.gr
> tevang3 at gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
> gmx-users mailing list gmx-users at gromacs.org
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Tsjerk A. Wassenaar, Ph.D.
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
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