Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[David van der Spoel]

On 22/09/15 07:42, Naba wrote:

Thank you Justin. I have to deduce some inference from this figure. Please
make me out about the following queries.

On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul  wrote:




On 9/21/15 4:00 AM, Naba wrote:


Dear Gromacs users and Developers,

I have performed dihedral PCA for 4 extracellular loops of a transmembrane
protein after successfully finishing 100 ns of simulation at 300 and 310
K.
I obtained figures for each loops for two different temperatures as in
this
link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .

As we can see in that figure that, the loop L1 has got only one minimum at
both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
also calculated the amount of frames in percentages at their respective
minima. It seems that L2 and L3 have got more number of frames at their
minima when combined in comparison to L1. Now my question is:

Can we say that L2 and L3 are tend to be more stable at 300K than that of
L1 at the both temperatures?



I wouldn't make any argument about "stability" here.



Then what can be concluded from this figure? Please hint some possible
explanations.
Dihedral PCA is tricky business. For instance the "volume" of phase 
space sampled in each grid point varies making it difficult to compare 
the probability per volume (which is related to the free energy).


The fact that the difference between 300K and 310K is so large proves 
your sampling is far from complete as well, so basically your results 
are inconclusive (e.g. you sample areas at 300K that you don't at 310K).




Conformational sampling, maybe, but the question is whether or not these
PCs are the same between the different simulations. If you're not
projecting one trajectory onto the other's eigenvectors, you're quite
possibly comparing apples and oranges.



The PCs are same for both simulations. I followed dPCA procedure as you
have explained in http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
. To obtained the 2D projections as in the link of the figure I issued the
following command for each and every loops:

g_anaeig -v eigenvec_L*.trr -f dangle_L*.trr -s resized_loop*.gro
-first 1 -last 2 -2d 2dproj_1_2.xvg

I think, I am comparing the same projections for both the simulations.




-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Naba]

Dear Gromacs users and Developers,

I have performed dihedral PCA for 4 extracellular loops of a transmembrane
protein after successfully finishing 100 ns of simulation at 300 and 310 K.
I obtained figures for each loops for two different temperatures as in this
link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .

As we can see in that figure that, the loop L1 has got only one minimum at
both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
also calculated the amount of frames in percentages at their respective
minima. It seems that L2 and L3 have got more number of frames at their
minima when combined in comparison to L1. Now my question is:

Can we say that L2 and L3 are tend to be more stable at 300K than that of
L1 at the both temperatures?
Please help.
Thanks in advance.

Regards

Nabajyoti Goswami

College of Veterinary Science
Khanapara, Guwahati 781022
Assam, India.
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Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Naba]

Thank you Justin. I have to deduce some inference from this figure. Please
make me out about the following queries.

On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul  wrote:

>
>
> On 9/21/15 4:00 AM, Naba wrote:
>
>> Dear Gromacs users and Developers,
>>
>> I have performed dihedral PCA for 4 extracellular loops of a transmembrane
>> protein after successfully finishing 100 ns of simulation at 300 and 310
>> K.
>> I obtained figures for each loops for two different temperatures as in
>> this
>> link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .
>>
>> As we can see in that figure that, the loop L1 has got only one minimum at
>> both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
>> also calculated the amount of frames in percentages at their respective
>> minima. It seems that L2 and L3 have got more number of frames at their
>> minima when combined in comparison to L1. Now my question is:
>>
>> Can we say that L2 and L3 are tend to be more stable at 300K than that of
>> L1 at the both temperatures?
>>
>
> I wouldn't make any argument about "stability" here.


Then what can be concluded from this figure? Please hint some possible
explanations.


> Conformational sampling, maybe, but the question is whether or not these
> PCs are the same between the different simulations. If you're not
> projecting one trajectory onto the other's eigenvectors, you're quite
> possibly comparing apples and oranges.
>

The PCs are same for both simulations. I followed dPCA procedure as you
have explained in http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
. To obtained the 2D projections as in the link of the figure I issued the
following command for each and every loops:

g_anaeig -v eigenvec_L*.trr -f dangle_L*.trr -s resized_loop*.gro
-first 1 -last 2 -2d 2dproj_1_2.xvg

I think, I am comparing the same projections for both the simulations.


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Justin Lemkul]

On 9/21/15 4:00 AM, Naba wrote:

Dear Gromacs users and Developers,

I have performed dihedral PCA for 4 extracellular loops of a transmembrane
protein after successfully finishing 100 ns of simulation at 300 and 310 K.
I obtained figures for each loops for two different temperatures as in this
link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .

As we can see in that figure that, the loop L1 has got only one minimum at
both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
also calculated the amount of frames in percentages at their respective
minima. It seems that L2 and L3 have got more number of frames at their
minima when combined in comparison to L1. Now my question is:

Can we say that L2 and L3 are tend to be more stable at 300K than that of
L1 at the both temperatures?


I wouldn't make any argument about "stability" here.  Conformational sampling, 
maybe, but the question is whether or not these PCs are the same between the 
different simulations.  If you're not projecting one trajectory onto the other's 
eigenvectors, you're quite possibly comparing apples and oranges.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Padmani Sandhu]

Sorry, I have posted my reply in wrong thread.

On Tuesday, September 22, 2015, Padmani Sandhu 
wrote:

> Hello justin,
>
> Thanks, actually I want to study movement of protons along the lenght of a
> water channel.
>
>
> Regards,
>
>
> Padmani
>
> On Monday, September 21, 2015, Justin Lemkul  > wrote:
>
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>
>
> --
> *Padmani sandhu*
> *Research Scholar,*
> *Center for Computational Biology and Bioinformatics,*
> *Central University of Himachal Pradesh,*
> *Temporary Academic Block, Shahpur *
> *Pin 176206, District Kangra,*
> *Himachal Pradesh, India*
>
>

-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[Padmani Sandhu]

Hello justin,

Thanks, actually I want to study movement of protons along the lenght of a
water channel.


Regards,


Padmani

On Monday, September 21, 2015, Justin Lemkul  wrote:

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> for Automatic Cleanup! (jalem...@vt.edu
> ) Add cleanup rule
> 
> | More info
> 
>


-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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