Re: [gmx-users] cosine content and nonconverged trajectory

[Justin Lemkul]

On 11/2/12 8:17 AM, ahmet yıldırım wrote:

Dear users,

The cosine content of the principal components is an effective
indicator for predicting whether or not a trajectory has been
convergent. A high cosine content typically indicates a nonconverged
trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven
Hayward and Bert L. de Groot).
What is a high cosine content? 0.2, 0.5 or 0.7 What is the value?



There have been numerous discussions on this topic in the past.  A few that come 
to mind immediately are in the following threads:


http://lists.gromacs.org/pipermail/gmx-users/2011-December/066921.html
http://lists.gromacs.org/pipermail/gmx-users/2012-April/070374.html

Check the list archive for more.

-Justin


Thanks in advance
--
Ahmet Yıldırım



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] cosine content and nonconverged trajectory

[ahmet yıldırım]

Dear users,

The cosine content of the principal components is an effective
indicator for predicting whether or not a trajectory has been
convergent. A high cosine content typically indicates a nonconverged
trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven
Hayward and Bert L. de Groot).
What is a high cosine content? 0.2, 0.5 or 0.7 What is the value?

Thanks in advance
--
Ahmet Yıldırım
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Re: [gmx-users] Cosine content

[Tsjerk Wassenaar]

Hey :)

This is pretty incorrect... A high cosine content is an indicator of
unidirectional motion in phase space. I've elaborated on that on this
list some while ago.

> Regarding your case, this means that, even if the RMSD is stable starting
> from 5ns, the protein still experiences "random" motions.

So the opposite is true: the protein configuration is adrift, i.e.,
it's undergoing conformational rearrangement, not random (thermal)
fluctuations. This rearrangement may happen in phase space far away
from the reference structure, thus not noticeable in the RMSD, which
will just say 'far away' (the larger the RMSD, the larger the volume
of phase space to be moving in).

> You should therefore consider as statistically relevant the trajectory
> starting from 30ns.

Arguable. The conformational rearrangement may be relevant and it may
even be a functional mode, which is just undersampled.

> Basing on my experience, I advice you to extend the simulation lenght
> (i.e.100ns) to ensure a larger dataset.

Of course, sampling longer makes sense :)


> Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto:

> I have a 50 ns trajectory and looking at the RMSD plot, i set aside the
> first  5 ns as the time required for stabilization and subsequently carried
> out a essential dynamics for the backbone atoms post 5ns.

It is very likely that equilibration of the system takes longer than
5ns. Actually it is highly unlikely that it has converged with 5ns.

>  But when i perform a cosine content analysis for the eigen vector 1, i get
> these strange results
>
> a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns )
> produces  a cosine value of 0.92

This suggests a transition. Look a the RMSD matrix for the trajectory
to see if you can spot a transition. As mentioned above, the
transition may be part of the equilibration, or reflect a functional
mode. That should be assessed using extended simulation(s).

>   but when i perform a cosine analysis using -b 5000 to -e 25000 ( 5-25ns) i
> get a cosine value of 0.24
>   also when i perform a cosine analysis using -b 3 to -- 5(30-50 ns)
> i get a cosine value of 0.05
>  so how should i interpret this result,

It's like doing PCA on the position of a canoe around a waterfall. If
you look at the whole stretch, including the drop down, you'll see the
thing getting closer to the fall more and more rapidly, taking the
plunge and then being pushed away from the fall. If you only look at
what happens before, there's just a slow drift towards the waterfall.
If you only look at the what happens after, the canoe is just wobbling
in the pond below randomly.

> does it imply that all the conformational changes are taking place between
> 30 to 50 ns 

No, there appears to be a conformational rearrangement before 30ns.
Likely most obvious between 20 and 30 ns. Again, look at the RMSD
matrix.

> or is there some thing wrong with the convergence of the system??? Papers
> tell that the cosine value does decreases with increased time scale due to
> enhanced sampling, but strange a 25 ns simulation has a low cosine value on
> the contrary a 50 ns simulation has an increased cosine value.

Nothing strange. It depends on the system and what is happening in it.
But it doesn't exclude the possibility of bad convergence.

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Cosine content

[Francesco Oteri]

Hi Vijayan,
cosine content should say how not-random are the movements observed in 
the configuration set you have analized.
Regarding your case, this means that, even if the RMSD is stable 
starting from 5ns, the protein still experiences "random" motions.
You should therefore consider as statistically relevant the trajectory 
starting from 30ns.
Basing on my experience, I advice you to extend the simulation lenght 
(i.e.100ns) to ensure a larger dataset.


Francesco


Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto:

Dear Gromacs users

I have a question regarding cosine content.

I have a 50 ns trajectory and looking at the RMSD plot, i set aside 
the first  5 ns as the time required for stabilization and 
subsequently carried out a essential dynamics for the backbone atoms 
post 5ns.


 But when i perform a cosine content analysis for the eigen vector 1, 
i get these strange results


a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns 
) produces  a cosine value of 0.92
  but when i perform a cosine analysis using -b 5000 to -e 25000 ( 
5-25ns) i get a cosine value of 0.24
  also when i perform a cosine analysis using -b 3 to -- 
5(30-50 ns) i get a cosine value of 0.05

 so how should i interpret this result,
does it imply that all the conformational changes are 
taking place between 30 to 50 ns 
or is there some thing wrong with the convergence of the system??? 
Papers tell that the cosine value does decreases with increased time 
scale due to enhanced sampling, but strange a 25 ns simulation has a 
low cosine value on the contrary a 50 ns simulation has an increased 
cosine value.


Regards
Vijayan.R



On Mon, Dec 12, 2011 at 5:31 PM, Justin A. Lemkul > wrote:




Alex Jemulin wrote:

Dear all
 Which is the difference between hydropilic and hydrophobic sas?


g_sas computes hydrophobic and hydrophilic surface area based on
the absolute value of the partial charge of the atom, which can be
adjusted with the -qmax flag.

How can give an interpretation to g_sas xvg graph?


Interpretation of the results is based on the question being asked
and the group being analyzed, things that only you know.

What can I find out in it and how can use g_sas to analyze a
trajectory?


Start by reading g_sas -h.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Cosine content

[R.S.K.Vijayan]

Dear Gromacs users

I have a question regarding cosine content.

I have a 50 ns trajectory and looking at the RMSD plot, i set aside the
first  5 ns as the time required for stabilization and subsequently carried
out a essential dynamics for the backbone atoms post 5ns.

 But when i perform a cosine content analysis for the eigen vector 1, i get
these strange results

a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns )
produces  a cosine value of 0.92
  but when i perform a cosine analysis using -b 5000 to -e 25000 ( 5-25ns)
i get a cosine value of 0.24
  also when i perform a cosine analysis using -b 3 to -- 5(30-50
ns) i get a cosine value of 0.05
 so how should i interpret this result,
does it imply that all the conformational changes are taking place between
30 to 50 ns 
or is there some thing wrong with the convergence of the system??? Papers
tell that the cosine value does decreases with increased time scale due to
enhanced sampling, but strange a 25 ns simulation has a low cosine value on
the contrary a 50 ns simulation has an increased cosine value.

Regards
Vijayan.R




On Mon, Dec 12, 2011 at 5:31 PM, Justin A. Lemkul  wrote:

>
>
> Alex Jemulin wrote:
>
>> Dear all
>>  Which is the difference between hydropilic and hydrophobic sas?
>>
>
> g_sas computes hydrophobic and hydrophilic surface area based on the
> absolute value of the partial charge of the atom, which can be adjusted
> with the -qmax flag.
>
>  How can give an interpretation to g_sas xvg graph?
>>
>
> Interpretation of the results is based on the question being asked and the
> group being analyzed, things that only you know.
>
>  What can I find out in it and how can use g_sas to analyze a trajectory?
>>
>>
>
> Start by reading g_sas -h.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] cosine content

[Kavyashree M]

Dear users,

   When are checking the cosine content of a PC, (Pls. Correct me if I am
wrong)
This is the command we use -
"g_analyze -f .xvg -cc .xvg"

and for first PC output says -
Cosine content of set 1 with 0.5 periods: ---

for nth PC also it says -
Cosine content of set 1 with 0.5 periods: ---

Where does this get the information that the cosine wave that it has to
fit is half the eigenvector rank? is it "y axis label" ?

Thank you
With regards
M. Kavyashree
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Re: [gmx-users] cosine content

[sunita]

Dear Tsjerk

Thanks for answering last question on finding eigenvectors.

Till now I have not received any answer for the following question.
What do you suggest for this?

Best regards,
Sunita

> Dear users,
>
> I am trying to calculate cosine content of the principal components using
> g_analyze.
>
> I am using time versus projection of trajectory along eigenvector 1
> (extracted from proj.xvg of g_anaeig) as an input file for g_analyze.
> When I calculated the same for eigenvector 2, got memory allocation
> problem.
> How can I fix it?
The second question is, am I doing correctly the calculation of cosine
content?
>
> Regards,
> Sunita
>
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[gmx-users] cosine content

[sunita]

Dear users,

I am trying to calculate cosine content of the principal components using
g_analyze.

I am using time versus projection of trajectory along eigenvector 1
(extracted from proj.xvg of g_anaeig) as an input file for g_analyze.
When I calculated the same for eigenvector 2, got memory allocation problem.
How can fix it?
Am I doing correctly the cosine content calculation?

Regards,
Sunita

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