[gmx-users] Internal Density

[Mark Abraham]

----- Original Message -----
From: abdullah ahmed <abdullah_renk_ahmed at hotmail.com>
Date: Friday, August 27, 2010 20:28
Subject: [gmx-users] Internal Density
To: gmx <gmx-users at gromacs.org>


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>  Dear all, 
> 
> I have 2 structures similar to a Beta-turn where the inside is hydrophobic, and I would like to find the density of just this part of the strucuture. More specifically, 
> both structure are identical expect for one mutation. One of the structures contains 2 glycines facing each other and the other contains a glycine facing a tryptophan.  
> I would like to know if there is a functionality in gromacs that can measure the difference of density between the two strucutres. 




First, you have to be able to define the volume of your region of interest. That will be neither easy nor unique. Presumably you want this local density as a surrogate for some other observable. Perhaps there is a better surrogate available...




Mark

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