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

Naba nabajyoti.goswami at gmail.com
Tue Sep 22 07:42:26 CEST 2015

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 <jalemkul at vt.edu> 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

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