[gmx-users] regarding the cosine content analysis

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 25 14:51:16 CET 2013 

Well, the cosine content doesn't tell you very much anyway. And
fitting a cosine with a full period to the second component only makes
sense if the first fits well to a half cosine. If the correlation
coefficient is about .1, it tells you less. It says nothing,
absolutely nothing about convergence and/or equilibrium.

Cheers,

Tsjerk

On Mon, Feb 25, 2013 at 2:36 PM, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:
> 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
>> >> > >> --
>> >> > >> gmx-users mailing list    gmx-users at gromacs.org
>> >> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > >> * Please search the archive at
>> >> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> >> > >> * Please don't post (un)subscribe requests to the list. Use the
>> >> > >> www interface or send it to gmx-users-request at gromacs.org.
>> >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> > >>
>> >> > >
>> >> > >
>> >> > >
>> >> > > --
>> >> > >
>> >> > >
>> ======================================================================
>> >> > >
>> >> > > 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
>> >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > > * Please search the archive at
>> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> > > * Please don't post (un)subscribe requests to the list. Use the
>> >> > > www interface or send it to gmx-users-request at gromacs.org.
>> >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Tsjerk A. Wassenaar, Ph.D.
>> >> >
>> >> > post-doctoral researcher
>> >> > Biocomputing Group
>> >> > Department of Biological Sciences
>> >> > 2500 University Drive NW
>> >> > Calgary, AB T2N 1N4
>> >> > Canada
>> >> > --
>> >> > gmx-users mailing list    gmx-users at gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > * Please search the archive at
>> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> > * Please don't post (un)subscribe requests to the list. Use the
>> >> > www interface or send it to gmx-users-request at gromacs.org.
>> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ======================================================================
>> >>
>> >> 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
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> * Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >
>> >
>> >
>> > --
>> > Ahmet Yıldırım
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Biocomputing Group
>> Department of Biological Sciences
>> 2500 University Drive NW
>> Calgary, AB T2N 1N4
>> Canada
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet Yıldırım
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

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

More information about the gromacs.org_gmx-users mailing list