[gmx-users] regarding the cosine content analysis

[Thomas Evangelidis]

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/
> > --
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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/