[gmx-users] regarding the cosine content analysis

Ahmet yıldırım ahmedo047 at gmail.com
Mon Feb 25 14:36:10 CET 2013 

Then, these cosine content's results are all normal?

2013/2/25 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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
> >> > >> --
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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/
> >> --
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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
> --
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-- 
Ahmet Yıldırım

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