[gmx-users] GridMatMD Result Interpretation

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 14 16:34:29 CEST 2009


To understand the figure, you should refer to ref. 12 in the GridMAT-MD paper 
(the original KALP-DPPC simulations by Kandasamy and Larson), which we used as a 
benchmark in developing the program, as well as the explanation in our Results 
section.  The purpose of the rainbow gradient is to easily represent bilayer 
deformation induced by the presence of some other chemical entity, in this case, 
a small peptide with negative hydrophobic mismatch.

The protein is not represented by blue; it is shown as a black ribbon.  The blue 
color around the protein indicates that the bilayer is "thinning" (i.e., 
reducing its vertical, z, dimension) due to hydrophobic mismatch.


Anirban Ghosh wrote:
> Hello Justin,
> I have a query regarding the interpretation of the results of GridMatMD. 
> In your paper you have given the eg. of KALP-DPPC simulation. The colour 
> index (blue to red) ranges from 2.5 to 4.5. Its the distance between the 
> P atoms of DPPC in the top and bottom layers i.e. the Z values. Right? 
> The protein is represented in Blue. Can you briefly explain this plot. I 
> mean what exactly is the significance of the variation in the colors 
> from blue to red i.e. from 2.5 to 4.5?
> Thanks a lot in advance.
> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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