[gmx-users] regarding the cosine content analysis

[Ahmet yıldırım]

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
> > >> --
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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