[gmx-users] regarding the cosine content analysis

[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, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:
> 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 <tevang3 at gmail.com>
>
>> On 25 February 2013 12:14, Tsjerk Wassenaar <tsjerkw at gmail.com> 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 first place. Looking at the cosine content to infer
>> >
>>
>> Yes, that's what I meant, to identity those ns where the protein does
>> unidirectional motion before it starts exploring the energy landscape, and
>> exclude them from the final analysis (whatever this is). At least this is
>> what I've seen doing in publications and this is what I have understood
>> from our previous conversations. I think your objection is about the way I
>> use the term "equilibration" to refer to what you call "relaxation" (I
>> presume it is not the same as energy minimization). Perhaps it would be
>> helpful to have your definition of the terms "equilibration" and
>> "relaxation.
>>
>>
>> > 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
>> > equilibrium.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> >
>> > 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.
>> > >
>> > > 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
>> > >> --
>> > >> gmx-users mailing list    gmx-users at gromacs.org
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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/
>> > > --
>> > > gmx-users mailing list    gmx-users at gromacs.org
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>> >
>> >
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>> >
>> > post-doctoral researcher
>> > Biocomputing Group
>> > Department of Biological Sciences
>> > 2500 University Drive NW
>> > Calgary, AB T2N 1N4
>> > Canada
>> > --
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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/
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>
>
>
> --
> Ahmet Yıldırım
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada